4V97

Crystal structure of the bacterial ribosome ram mutation G299A.

• PDB DOI: https://doi.org/10.2210/pdb4V97/pdb
• Entry: 4V97 supersedes: 4EJ9, 4EJA, 4EJB, 4EJC
• NAKB: 4V97

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8, Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2012-04-06 Released: 2014-07-09 
• Deposition Author(s): Fagan, C.E., Dunkle, J.A., Maehigashi, T., Dunham, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.52 Å
• R-Value Free: 0.249 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Models: experimental

Literature

Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.

Fagan, C.E., Dunkle, J.A., Maehigashi, T., Dang, M.N., Devaraj, A., Miles, S.J., Qin, D., Fredrick, K., Dunham, C.M.

(2013) Proc Natl Acad Sci U S A 110: 9716-9721

• PubMed: 23630274 
• DOI: https://doi.org/10.1073/pnas.1301585110
• Primary Citation of Related Structures:  
  4V8J, 4V97


• PubMed Abstract: 
  

  After four decades of research aimed at understanding tRNA selection on the ribosome, the mechanism by which ribosomal ambiguity (ram) mutations promote miscoding remains unclear. Here, we present two X-ray crystal structures of the Thermus thermophilus 70S ribosome containing 16S rRNA ram mutations, G347U and G299A. Each of these mutations causes miscoding in vivo and stimulates elongation factor thermo unstable (EF-Tu)-dependent GTP hydrolysis in vitro. Mutation G299A is located near the interface of ribosomal proteins S4 and S5 on the solvent side of the subunit, whereas G347U is located 77 Å distant, at intersubunit bridge B8, close to where EF-Tu engages the ribosome. Despite these disparate locations, both mutations induce almost identical structural rearrangements that disrupt the B8 bridge--namely, the interaction of h8/h14 with L14 and L19. This conformation most closely resembles that seen upon EF-Tu-GTP-aminoacyl-tRNA binding to the 70S ribosome. These data provide evidence that disruption and/or distortion of B8 is an important aspect of GTPase activation. We propose that, by destabilizing B8, G299A and G347U reduce the energetic cost of attaining the GTPase-activated state and thereby decrease the stringency of decoding. This previously unappreciated role for B8 in controlling the decoding process may hold relevance for many other ribosomal mutations known to influence translational fidelity.

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Organizational Affiliation: 

Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4,576.93 kDa 
• Atom Count: 293,977 
• Modelled Residue Count: 21,184 
• Deposited Residue Count: 22,210 
• Unique protein chains: 50
• Unique nucleic acid chains: 6

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B [auth AB], GB [auth CB]	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C [auth AC], HB [auth CC]	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D [auth AD], IB [auth CD]	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E [auth AE], JB [auth CE]	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F [auth AF], KB [auth CF]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G [auth AG], LB [auth CG]	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H [auth AH], MB [auth CH]	138	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I [auth AI], NB [auth CI]	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J [auth AJ], OB [auth CJ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K [auth AK], PB [auth CK]	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L [auth AL], QB [auth CL]	132	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3  Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M [auth AM], RB [auth CM]	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	N [auth AN], SB [auth CN]	61	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O [auth AO], TB [auth CO]	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P [auth AP], UB [auth CP]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q [auth AQ], VB [auth CQ]	105	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R [auth AR], WB [auth CR]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S [auth AS], XB [auth CS]	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T [auth AT], YB [auth CT]	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	U [auth AU], ZB [auth CU]	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L1	BA [auth BC], GC [auth DC]	229	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP7  Go to UniProtKB:  Q5SLP7

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L2	CA [auth BD], HC [auth DD]	276	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60405  Go to UniProtKB:  P60405

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L3	DA [auth BE], IC [auth DE]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN8  Go to UniProtKB:  Q5SHN8

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L4	EA [auth BF], JC [auth DF]	210	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN9  Go to UniProtKB:  Q5SHN9

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L5	FA [auth BG], KC [auth DG]	182	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ0  Go to UniProtKB:  Q5SHQ0

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L6	GA [auth BH], LC [auth DH]	180	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L9	HA [auth BI], MC [auth DI]	148	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ1  Go to UniProtKB:  Q5SLQ1

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L13	IA [auth BN], NC [auth DN]	140	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60488  Go to UniProtKB:  P60488

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L14	JA [auth BO], OC [auth DO]	122	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP8  Go to UniProtKB:  Q5SHP8

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L15	KA [auth BP], PC [auth DP]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ7  Go to UniProtKB:  Q5SHQ7

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L16	LA [auth BQ], QC [auth DQ]	141	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60489  Go to UniProtKB:  P60489

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L17	MA [auth BR], RC [auth DR]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5  Go to UniProtKB:  Q9Z9H5

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L18	NA [auth BS], SC [auth DS]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ4  Go to UniProtKB:  Q5SHQ4

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L19	OA [auth BT], TC [auth DT]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60490  Go to UniProtKB:  P60490

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L20	PA [auth BU], UC [auth DU]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60491  Go to UniProtKB:  P60491

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L21	QA [auth BV], VC [auth DV]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60492  Go to UniProtKB:  P60492

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L22	RA [auth BW], WC [auth DW]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP3  Go to UniProtKB:  Q5SHP3

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L23	SA [auth BX], XC [auth DX]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP0  Go to UniProtKB:  Q5SHP0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L24	TA [auth BY], YC [auth DY]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP9  Go to UniProtKB:  Q5SHP9

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L25	UA [auth BZ], ZC [auth DZ]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ1  Go to UniProtKB:  Q5SHZ1

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L27	AD [auth D0], VA [auth B0]	85	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60493  Go to UniProtKB:  P60493

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L28	BD [auth D1], WA [auth B1]	98	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60494  Go to UniProtKB:  P60494

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L29	CD [auth D2], XA [auth B2]	72	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP6  Go to UniProtKB:  Q5SHP6

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L30	DD [auth D3], YA [auth B3]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ6  Go to UniProtKB:  Q5SHQ6

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L31	ED [auth D4], ZA [auth B4]	71	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJE1  Go to UniProtKB:  Q5SJE1

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L32	AB [auth B5], FD [auth D5]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80339  Go to UniProtKB:  P80339

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L33	BB [auth B6], GD [auth D6]	54	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P35871  Go to UniProtKB:  P35871

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L34	CB [auth B7], HD [auth D7]	49	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80340  Go to UniProtKB:  P80340

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L35	DB [auth B8], ID [auth D8]	65	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKU1  Go to UniProtKB:  Q5SKU1

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L36	EB [auth B9], JD [auth D9]	37	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR2  Go to UniProtKB:  Q5SHR2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A [auth AA], FB [auth CA]	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
P-SITE tRNA fMet	AC [auth CV], V [auth AV]	77	Escherichia coli K-12

Entity ID: 23
Molecule	Chains	Length	Organism	Image
E-SITE TRNA PHE OR A-SITE tRNA Phe	BC [auth CW], DC [auth CY], W [auth AW], Y [auth AY]	76	Escherichia coli K-12

Entity ID: 24
Molecule	Chains	Length	Organism	Image
mRNA	CC [auth CX], X [auth AX]	24	N/A

Entity ID: 25
Molecule	Chains	Length	Organism	Image
23S rRNA	EC [auth DA], Z [auth BA]	2,915	Thermus thermophilus HB8

Entity ID: 26
Molecule	Chains	Length	Organism	Image
5S rRNA	AA [auth BB], FC [auth DB]	122	Thermus thermophilus HB8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAR	MAA [auth CA], QH [auth AA]	PAROMOMYCIN C23 H45 N5 O14 UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN	OAA [auth CD], RAA [auth CN], RH [auth AD], TH [auth AN]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth CA], ABA [auth DA], ACA [auth DA], ADA [auth DA], AE [auth AA], AEA [auth DA], AF [auth AA], AFA [auth DA], AG [auth AA], AGA [auth DA], AH [auth AA], AHA [auth DA], AI [auth BA], AIA [auth DA], AJ [auth BA], AJA [auth DA], AK [auth BA], AKA [auth DA], AL [auth BA], ALA [auth DA], AM [auth BA], AMA [auth DA], AN [auth BA], ANA [auth DA], AO [auth BA], AOA [auth DA], AP [auth BA], APA [auth DA], AQ [auth BA], AQA [auth DA], AR [auth BA], ARA [auth DX], AS [auth BA], AT [auth BA], AU [auth BA], AV [auth B5], AW [auth CA], AX [auth CA], AY [auth CA], AZ [auth CA], BAA [auth CA], BBA [auth DA], BCA [auth DA], BDA [auth DA], BE [auth AA], BEA [auth DA], BF [auth AA], BFA [auth DA], BG [auth AA], BGA [auth DA], BH [auth AA], BHA [auth DA], BI [auth BA], BIA [auth DA], BJ [auth BA], BJA [auth DA], BK [auth BA], BKA [auth DA], BL [auth BA], BLA [auth DA], BM [auth BA], BMA [auth DA], BN [auth BA], BNA [auth DA], BO [auth BA], BOA [auth DA], BP [auth BA], BPA [auth DA], BQ [auth BA], BQA [auth DA], BR [auth BA], BRA [auth D0], BS [auth BA], BT [auth BA], BU [auth BA], BV [auth B7], BW [auth CA], BX [auth CA], BY [auth CA], BZ [auth CA], CAA [auth CA], CBA [auth DA], CCA [auth DA], CDA [auth DA], CE [auth AA], CEA [auth DA], CF [auth AA], CFA [auth DA], CG [auth AA], CGA [auth DA], CH [auth AA], CHA [auth DA], CI [auth BA], CIA [auth DA], CJ [auth BA], CJA [auth DA], CK [auth BA], CKA [auth DA], CL [auth BA], CLA [auth DA], CM [auth BA], CMA [auth DA], CN [auth BA], CNA [auth DA], CO [auth BA], COA [auth DA], CP [auth BA], CPA [auth DA], CQ [auth BA], CQA [auth DA], CR [auth BA], CRA [auth D0], CS [auth BA], CT [auth BA], CU [auth BA], CV [auth CA], CW [auth CA], CX [auth CA], CY [auth CA], CZ [auth CA], DAA [auth CA], DBA [auth DA], DCA [auth DA], DDA [auth DA], DE [auth AA], DEA [auth DA], DF [auth AA], DFA [auth DA], DG [auth AA], DGA [auth DA], DH [auth AA], DHA [auth DA], DI [auth BA], DIA [auth DA], DJ [auth BA], DJA [auth DA], DK [auth BA], DKA [auth DA], DL [auth BA], DLA [auth DA], DM [auth BA], DMA [auth DA], DN [auth BA], DNA [auth DA], DO [auth BA], DOA [auth DA], DP [auth BA], DPA [auth DA], DQ [auth BA], DQA [auth DA], DR [auth BA], DRA [auth D1], DS [auth BA], DT [auth BA], DU [auth BA], DV [auth CA], DW [auth CA], DX [auth CA], DY [auth CA], DZ [auth CA], EAA [auth CA], EBA [auth DA], ECA [auth DA], EDA [auth DA], EE [auth AA], EEA [auth DA], EF [auth AA], EFA [auth DA], EG [auth AA], EGA [auth DA], EH [auth AA], EHA [auth DA], EI [auth BA], EIA [auth DA], EJ [auth BA], EJA [auth DA], EK [auth BA], EKA [auth DA], EL [auth BA], ELA [auth DA], EM [auth BA], EMA [auth DA], EN [auth BA], ENA [auth DA], EO [auth BA], EOA [auth DA], EP [auth BA], EPA [auth DA], EQ [auth BA], EQA [auth DA], ER [auth BA], ERA [auth D1], ES [auth BA], ET [auth BA], EU [auth BA], EV [auth CA], EW [auth CA], EX [auth CA], EY [auth CA], EZ [auth CA], FAA [auth CA], FBA [auth DA], FCA [auth DA], FDA [auth DA], FE [auth AA], FEA [auth DA], FF [auth AA], 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[auth CA], GX [auth CA], GY [auth CA], GZ [auth CA], HAA [auth CA], HBA [auth DA], HCA [auth DA], HDA [auth DA], HE [auth AA], HEA [auth DA], HF [auth AA], HFA [auth DA], HG [auth AA], HGA [auth DA], HH [auth AA], HHA [auth DA], HI [auth BA], HIA [auth DA], HJ [auth BA], HJA [auth DA], HK [auth BA], HKA [auth DA], HL [auth BA], HLA [auth DA], HM [auth BA], HMA [auth DA], HN [auth BA], HNA [auth DA], HO [auth BA], HOA [auth DA], HP [auth BA], HPA [auth DA], HQ [auth BA], HQA [auth DB], HR [auth BA], HRA [auth D5], HS [auth BA], HT [auth BA], HU [auth BA], HV [auth CA], HW [auth CA], HX [auth CA], HY [auth CA], HZ [auth CA], IAA [auth CA], IBA [auth DA], ICA [auth DA], IDA [auth DA], IE [auth AA], IEA [auth DA], IF [auth AA], IFA [auth DA], IG [auth AA], IGA [auth DA], IH [auth AA], IHA [auth DA], II [auth BA], IIA [auth DA], IJ [auth BA], IJA [auth DA], IK [auth BA], IKA [auth DA], IL [auth BA], ILA [auth DA], IM [auth BA], IMA [auth DA], IN [auth BA], INA [auth DA], IO [auth BA], IOA [auth DA], IP [auth BA], IPA [auth DA], IQ [auth BA], IQA [auth DB], IR [auth BA], IRA [auth D8], IS [auth BA], IT [auth BA], IU [auth BA], IV [auth CA], IW [auth CA], IX [auth CA], IY [auth CA], IZ [auth CA], JAA [auth CA], JBA [auth DA], JCA [auth DA], JDA [auth DA], JE [auth AA], JEA [auth DA], JF [auth AA], JFA [auth DA], JG [auth AA], JGA [auth DA], JH [auth AA], JHA [auth DA], JI [auth BA], JIA [auth DA], JJ [auth BA], JJA [auth DA], JK [auth BA], JKA [auth DA], JL [auth BA], JLA [auth DA], JM [auth BA], JMA [auth DA], JN [auth BA], JNA [auth DA], JO [auth BA], JOA [auth DA], JP [auth BA], JPA [auth DA], JQ [auth BA], JQA [auth DB], JR [auth BA], JS [auth BA], JT [auth BA], JU [auth BA], JV [auth CA], JW [auth CA], JX [auth CA], JY [auth CA], JZ [auth CA], KAA [auth CA], KBA [auth DA], KCA [auth DA], KD [auth AA], KDA [auth DA], KE [auth AA], KEA [auth DA], KF [auth AA], KFA [auth DA], KG [auth AA], KGA [auth DA], KH [auth AA], KHA [auth DA], KI [auth BA], KIA [auth DA], KJ [auth BA], KJA [auth DA], KK [auth BA], KKA [auth DA], KL [auth BA], KLA [auth DA], KM [auth BA], KMA [auth DA], KN [auth BA], KNA [auth DA], KO [auth BA], KOA [auth DA], KP [auth BA], KPA [auth DA], KQ [auth BA], KQA [auth DB], KR [auth BA], KS [auth BA], KT [auth BA], KU [auth BA], KV [auth CA], KW [auth CA], KX [auth CA], KY [auth CA], KZ [auth CA], LAA [auth CA], LBA [auth DA], LCA [auth DA], LD [auth AA], LDA [auth DA], LE [auth AA], LEA [auth DA], LF [auth AA], LFA [auth DA], LG [auth AA], LGA [auth DA], LH [auth AA], LHA [auth DA], LI [auth BA], LIA [auth DA], LJ [auth BA], LJA [auth DA], LK [auth BA], LKA [auth DA], LL [auth BA], LLA [auth DA], LM [auth BA], LMA [auth DA], LN [auth BA], LNA [auth DA], LO [auth BA], LOA [auth DA], LP [auth BA], LPA [auth DA], LQ [auth BA], LQA [auth DB], LR [auth BA], LS [auth BA], LT [auth BA], LU [auth BB], LV [auth CA], LW [auth CA], LX [auth CA], LY [auth CA], LZ [auth CA], MBA [auth DA], MCA [auth DA], MD [auth AA], MDA [auth DA], ME [auth AA], MEA [auth DA], MF [auth AA], MFA [auth DA], MG [auth AA], MGA [auth DA], MH [auth AA], MHA [auth DA], MI [auth BA], MIA [auth DA], MJ [auth BA], MJA [auth DA], MK [auth BA], MKA [auth DA], ML [auth BA], MLA [auth DA], MM [auth BA], MMA [auth DA], MN [auth BA], MNA [auth DA], MO [auth BA], MOA [auth DA], MP [auth BA], MPA [auth DA], MQ [auth BA], MQA [auth DD], MR [auth BA], MS [auth BA], MT [auth BA], MU [auth BB], MV [auth CA], MW [auth CA], MX [auth CA], MY [auth CA], MZ [auth CA], NAA [auth CA], NBA [auth DA], NCA [auth DA], ND [auth AA], NDA [auth DA], NE [auth AA], NEA [auth DA], NF [auth AA], NFA [auth DA], NG [auth AA], NGA [auth DA], NH [auth AA], NHA [auth DA], NI [auth BA], NIA [auth DA], NJ [auth BA], NJA [auth DA], NK [auth BA], NKA [auth DA], NL [auth BA], NLA [auth DA], NM [auth BA], NMA [auth DA], NN [auth BA], NNA [auth DA], NO [auth BA], NOA [auth DA], NP [auth BA], NPA [auth DA], NQ [auth BA], NQA [auth DD], NR [auth BA], NS [auth BA], NT [auth BA], NU [auth BB], NV [auth CA], NW [auth CA], NX [auth CA], NY [auth CA], NZ [auth CA], OBA [auth DA], OCA [auth DA], OD [auth AA], ODA [auth DA], OE [auth AA], OEA [auth DA], OF [auth AA], OFA [auth DA], OG [auth AA], OGA [auth DA], OH [auth AA], OHA [auth DA], OI [auth BA], OIA [auth DA], OJ [auth BA], OJA [auth DA], OK [auth BA], OKA [auth DA], OL [auth BA], OLA [auth DA], OM [auth BA], OMA [auth DA], ON [auth BA], ONA [auth DA], OO [auth BA], OOA [auth DA], OP [auth BA], OPA [auth DA], OQ [auth BA], OQA [auth DD], OR [auth BA], OS [auth BA], OT [auth BA], OU [auth BB], OV [auth CA], OW [auth CA], OX [auth CA], OY [auth CA], OZ [auth CA], PAA [auth CE], PBA [auth DA], PCA [auth DA], PD [auth AA], PDA [auth DA], PE [auth AA], PEA [auth DA], PF [auth AA], PFA [auth DA], PG [auth AA], PGA [auth DA], PH [auth AA], PHA [auth DA], PI [auth BA], PIA [auth DA], PJ [auth BA], PJA [auth DA], PK [auth BA], PKA [auth DA], PL [auth BA], PLA [auth DA], PM [auth BA], PMA [auth DA], PN [auth BA], PNA [auth DA], PO [auth BA], POA [auth DA], PP [auth BA], PPA [auth DA], PQ [auth BA], PQA [auth DE], PR [auth BA], PS [auth BA], PT [auth BA], PU [auth BB], PV [auth CA], PW [auth CA], PX [auth CA], PY [auth CA], PZ [auth CA], QAA [auth CE], QBA [auth DA], QCA [auth DA], QD [auth AA], QDA [auth DA], QE [auth AA], QEA [auth DA], QF [auth AA], QFA [auth DA], QG [auth AA], QGA [auth DA], QHA [auth DA], QI [auth BA], QIA [auth DA], QJ [auth BA], QJA [auth DA], QK [auth BA], QKA [auth DA], QL [auth BA], QLA [auth DA], QM [auth BA], QMA [auth DA], QN [auth BA], QNA [auth DA], QO [auth BA], QOA [auth DA], QP [auth BA], QPA [auth DA], QQ [auth BA], QQA [auth DE], QR [auth BA], QS [auth BA], QT [auth BA], QU [auth BD], QV [auth CA], QW [auth CA], QX [auth CA], QY [auth CA], QZ [auth CA], RBA [auth DA], RCA [auth DA], RD [auth AA], RDA [auth DA], RE [auth AA], REA [auth DA], RF [auth AA], RFA [auth DA], RG [auth AA], RGA [auth DA], RHA [auth DA], RI [auth BA], RIA [auth DA], RJ [auth BA], RJA [auth DA], RK [auth BA], RKA [auth DA], RL [auth BA], RLA [auth DA], RM [auth BA], RMA [auth DA], RN [auth BA], RNA [auth DA], RO [auth BA], ROA [auth DA], RP [auth BA], RPA [auth DA], RQ [auth BA], RQA [auth DF], RR [auth BA], RS [auth BA], RT [auth BA], RU [auth BD], RV [auth CA], RW [auth CA], RX [auth CA], RY [auth CA], RZ [auth CA], SAA [auth CV], SBA [auth DA], SCA [auth DA], SD [auth AA], SDA [auth DA], SE [auth AA], SEA [auth DA], SF [auth AA], SFA [auth DA], SG [auth AA], SGA [auth DA], SH [auth AE], SHA [auth DA], SI [auth BA], SIA [auth DA], SJ [auth BA], SJA [auth DA], SK [auth BA], SKA [auth DA], SL [auth BA], SLA [auth DA], SM [auth BA], SMA [auth DA], SN [auth BA], SNA [auth DA], SO [auth BA], SOA [auth DA], SP [auth BA], SPA [auth DA], SQ [auth BA], SQA [auth DP], SR [auth BA], SS [auth BA], ST [auth BA], SU [auth BE], SV [auth CA], SW [auth CA], SX [auth CA], SY [auth CA], SZ [auth CA], TAA [auth CV], TBA [auth DA], TCA [auth DA], TD [auth AA], TDA [auth DA], TE [auth AA], TEA [auth DA], TF [auth AA], TFA [auth DA], TG [auth AA], TGA [auth DA], THA [auth DA], TI [auth BA], TIA [auth DA], TJ [auth BA], TJA [auth DA], TK [auth BA], TKA [auth DA], TL [auth BA], TLA [auth DA], TM [auth BA], TMA [auth DA], TN [auth BA], TNA [auth DA], TO [auth BA], TOA [auth DA], TP [auth BA], TPA [auth DA], TQ [auth BA], TQA [auth DP], TR [auth BA], TS [auth BA], TT [auth BA], TU [auth BE], TV [auth CA], TW [auth CA], TX [auth CA], TY [auth CA], TZ [auth CA], UAA [auth CV], UBA [auth DA], UCA [auth DA], UD [auth AA], UDA [auth DA], UE [auth AA], UEA [auth DA], UF [auth AA], UFA [auth DA], UG [auth AA], UGA [auth DA], UH [auth AV], UHA [auth DA], UI [auth BA], UIA [auth DA], UJ [auth BA], UJA [auth DA], UK [auth BA], UKA [auth DA], UL [auth BA], ULA [auth DA], UM [auth BA], UMA [auth DA], UN [auth BA], UNA [auth DA], UO [auth BA], UOA [auth DA], UP [auth BA], UPA [auth DA], UQ [auth BA], UQA [auth DP], UR [auth BA], US [auth BA], UT [auth BA], UU [auth BE], UV [auth CA], UW [auth CA], UX [auth CA], UY [auth CA], UZ [auth CA], VAA [auth CV], VBA [auth DA], VCA [auth DA], VD [auth AA], VDA [auth DA], VE [auth AA], VEA [auth DA], VF [auth AA], VFA [auth DA], VG [auth AA], VGA [auth DA], VH [auth AV], VHA [auth DA], VI [auth BA], VIA [auth DA], VJ [auth BA], VJA [auth DA], VK [auth BA], VKA [auth DA], VL [auth BA], VLA [auth DA], VM [auth BA], VMA [auth DA], VN [auth BA], VNA [auth DA], VO [auth BA], VOA [auth DA], VP [auth BA], VPA [auth DA], VQ [auth BA], VQA [auth DQ], VR [auth BA], VS [auth BA], VT [auth BA], VU [auth BF], VV [auth CA], VW [auth CA], VX [auth CA], VY [auth CA], VZ [auth CA], WAA [auth CV], WBA [auth DA], WCA [auth DA], WD [auth AA], WDA [auth DA], WE [auth AA], WEA [auth DA], WF [auth AA], WFA [auth DA], WG [auth AA], WGA [auth DA], WH [auth AV], WHA [auth DA], WI [auth BA], WIA [auth DA], WJ [auth BA], WJA [auth DA], WK [auth BA], WKA [auth DA], WL [auth BA], WLA [auth DA], WM [auth BA], WMA [auth DA], WN [auth BA], WNA [auth DA], WO [auth BA], WOA [auth DA], WP [auth BA], WPA [auth DA], WQ [auth BA], WQA [auth DU], WR [auth BA], WS [auth BA], WT [auth BA], WU [auth BN], WV [auth CA], WW [auth CA], WX [auth CA], WY [auth CA], WZ [auth CA], XAA [auth CW], XBA [auth DA], XCA [auth DA], XD [auth AA], XDA [auth DA], XE [auth AA], XEA [auth DA], XF [auth AA], XFA [auth DA], XG [auth AA], XGA [auth DA], XH [auth AV], XHA [auth DA], XI [auth BA], XIA [auth DA], XJ [auth BA], XJA [auth DA], XK [auth BA], XKA [auth DA], XL [auth BA], XLA [auth DA], XM [auth BA], XMA [auth DA], XN [auth BA], XNA [auth DA], XO [auth BA], XOA [auth DA], XP [auth BA], XPA [auth DA], XQ [auth BA], XQA [auth DU], XR [auth BA], XS [auth BA], XT [auth BA], XU [auth BO], XV [auth CA], XW [auth CA], XX [auth CA], XY [auth CA], XZ [auth CA], YAA [auth CX], YBA [auth DA], YCA [auth DA], YD [auth AA], YDA [auth DA], YE [auth AA], YEA [auth DA], YF [auth AA], YFA [auth DA], YG [auth AA], YGA [auth DA], YH [auth AV], YHA [auth DA], YI [auth BA], YIA [auth DA], YJ [auth BA], YJA [auth DA], YK [auth BA], YKA [auth DA], YL [auth BA], YLA [auth DA], YM [auth BA], YMA [auth DA], YN [auth BA], YNA [auth DA], YO [auth BA], YOA [auth DA], YP [auth BA], YPA [auth DA], YQ [auth BA], YQA [auth DU], YR [auth BA], YS [auth BA], YT [auth BA], YU [auth BP], YV [auth CA], YW [auth CA], YX [auth CA], YY [auth CA], YZ [auth CA], ZAA [auth CY], ZBA [auth DA], ZCA [auth DA], ZD [auth AA], ZDA [auth DA], ZE [auth AA], ZEA [auth DA], ZF [auth AA], ZFA [auth DA], ZG [auth AA], ZGA [auth DA], ZH [auth AX], ZHA [auth DA], ZI [auth BA], ZIA [auth DA], ZJ [auth BA], ZJA [auth DA], ZK [auth BA], ZKA [auth DA], ZL [auth BA], ZLA [auth DA], ZM [auth BA], ZMA [auth DA], ZN [auth BA], ZNA [auth DA], ZO [auth BA], ZOA [auth DA], ZP [auth BA], ZPA [auth DA], ZQ [auth BA], ZQA [auth DW], ZR [auth BA], ZS [auth BA], ZT [auth BA], ZU [auth BU], ZV [auth CA], ZW [auth CA], ZX [auth CA], ZY [auth CA], ZZ [auth CA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.52 Å
• R-Value Free: 0.249 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.459	α = 90
b = 447.344	β = 90
c = 622.298	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Fagan, C.E., Dunkle, J.A., Maehigashi, T., Dunham, C.M.
• This entry supersedes: 4EJ9, 4EJA, 4EJB, 4EJC

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary