4V5K

Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome

• PDB DOI: https://doi.org/10.2210/pdb4V5K/pdb
• Entry: 4V5K supersedes: 2XFZ, 2XG0, 2XG1, 2XG2
• NAKB: 4V5K

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


• Deposited: 2010-05-29 Released: 2014-07-09 
• Deposition Author(s): Ng, C.L., Lang, K., Meenan, N.A.G., Sharma, A., Kelley, A.C., Kleanthous, C., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Literature

Structural Basis for 16S Ribosomal RNA Cleavage by the Cytotoxic Domain of Colicin E3.

Ng, C.L., Lang, K., Meenan, N.A.G., Sharma, A., Kelley, A.C., Kleanthous, C., Ramakrishnan, V.

(2010) Nat Struct Mol Biol 17: 1241-1246

• PubMed: 20852642 
• DOI: https://doi.org/10.1038/nsmb.1896
• Primary Citation of Related Structures:  
  4V5K


• PubMed Abstract: 
  

  The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves the 16S ribosomal RNA (rRNA) between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3. These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 52-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 52-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 52-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 52-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4,561.56 kDa 
• Atom Count: 296,762 
• Modelled Residue Count: 21,560 
• Deposited Residue Count: 22,390 
• Unique protein chains: 52
• Unique nucleic acid chains: 6

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S2	B [auth AB], HB [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], IB [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], JB [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], KB [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], LB [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], MB [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], NB [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], OB [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], PB [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], QB [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], RB [auth CL]	135	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], SB [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], TB [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], UB [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], VB [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], WB [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], XB [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], YB [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], ZB [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	AC [auth CU], U [auth AU]	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: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
COLICIN-E3	EC [auth CY], Y [auth AY]	97	Escherichia coli	Mutation(s): 1  EC: 4.6.1
UniProt
Find proteins for P00646 (Escherichia coli) Explore P00646  Go to UniProtKB:  P00646

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L27	FC [auth D0], Z [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: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L28	AA [auth B1], GC [auth D1]	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: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L29	BA [auth B2], HC [auth D2]	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: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L30	CA [auth B3], IC [auth D3]	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: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L31	DA [auth B4], JC [auth D4]	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: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L32	EA [auth B5], KC [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: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L33	FA [auth B6], LC [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: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L34	GA [auth B7], MC [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: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L35	HA [auth B8], NC [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: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L36	IA [auth B9], OC [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: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L1	LA [auth BC], RC [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: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L2	MA [auth BD], SC [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: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L3	NA [auth BE], TC [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: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L4	OA [auth BF], UC [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: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L5	PA [auth BG], VC [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: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L6	QA [auth BH], WC [auth DH]	180	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L9	RA [auth BI], XC [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: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L10	SA [auth BJ], YC [auth DJ]	131	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L13	TA [auth BN], ZC [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: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L14	AD [auth DO], UA [auth BO]	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: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L15	BD [auth DP], VA [auth BP]	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: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L16	CD [auth DQ], WA [auth BQ]	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: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L17	DD [auth DR], XA [auth BR]	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: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L18	ED [auth DS], YA [auth BS]	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: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L19	FD [auth DT], ZA [auth BT]	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: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L20	AB [auth BU], GD [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: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L21	BB [auth BV], HD [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: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L22	CB [auth BW], ID [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: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L23	DB [auth BX], JD [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: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L24	EB [auth BY], KD [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: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L25	FB [auth BZ], LD [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: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A [auth AA], GB [auth CA]	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
E-SITE TRNA PHE OR P-SITE TRNA PHE	BC [auth CV], CC [auth CW], V [auth AV], W [auth AW]	77	Escherichia coli K-12

Entity ID: 23
Molecule	Chains	Length	Organism	Image
MRNA	X [auth AX]	25	synthetic construct

Entity ID: 35
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	JA [auth BA], PC [auth DA]	2,848	Thermus thermophilus HB8

Entity ID: 36
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	KA [auth BB], QC [auth DB]	122	Thermus thermophilus HB8

Entity ID: 58
Molecule	Chains	Length	Organism	Image
MRNA	DC [auth CX]	25	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	BS [auth AD], MS [auth AN], ODB [auth CD], XR [auth AD]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth BA], AAB [auth CA], AAC [auth DA], ABA [auth BA], ABB [auth CA], ABC [auth DA], ACA [auth BA], ACB [auth CA], ACC [auth DA], ADA [auth BA], ADB [auth CA], ADC [auth DA], AE [auth AA], AEA [auth BA], AEB [auth CV], AEC [auth DA], AF [auth AA], AFA [auth BA], AFB [auth D7], AFC [auth DA], AG [auth AA], AGA [auth BA], AGB [auth DA], AGC [auth DA], AH [auth AA], AHA [auth BA], AHB [auth DA], AHC [auth DA], AI [auth AA], AIA [auth BA], AIB [auth DA], AIC [auth DA], AJ [auth AA], AJA [auth BA], AJB [auth DA], AJC [auth DA], AK [auth AA], AKA [auth BA], AKB [auth DA], AKC [auth DA], AL [auth AA], ALA [auth BA], ALB [auth DA], ALC [auth DA], AM [auth AA], AMA [auth BA], AMB [auth DA], AMC [auth DA], AN [auth AA], ANA [auth BA], ANB [auth DA], ANC [auth DA], AO [auth AA], AOA [auth BA], AOB [auth DA], AOC [auth DB], AP [auth AA], APA [auth BA], APB [auth DA], APC [auth DP], AQ [auth AA], AQA [auth BA], AQB [auth DA], AR [auth AA], ARA [auth BA], ARB [auth DA], AS [auth AD], ASA 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[auth DA], PD [auth AA], PDA [auth BA], PDB [auth CD], PDC [auth DA], PE [auth AA], PEA [auth BA], PEB [auth D0], PEC [auth DA], PF [auth AA], PFA [auth BA], PFB [auth DA], PFC [auth DA], PG [auth AA], PGA [auth BA], PGB [auth DA], PGC [auth DA], PH [auth AA], PHA [auth BA], PHB [auth DA], PHC [auth DA], PI [auth AA], PIA [auth BA], PIB [auth DA], PIC [auth DA], PJ [auth AA], PJA [auth BA], PJB [auth DA], PJC [auth DA], PK [auth AA], PKA [auth BA], PKB [auth DA], PKC [auth DA], PL [auth AA], PLA [auth BA], PLB [auth DA], PLC [auth DA], PM [auth AA], PMA [auth BA], PMB [auth DA], PMC [auth DA], PN [auth AA], PNA [auth BA], PNB [auth DA], PNC [auth DA], PO [auth AA], POA [auth BA], POB [auth DA], POC [auth DF], PP [auth AA], PPA [auth BA], PPB [auth DA], PQ [auth AA], PQA [auth BA], PQB [auth DA], PR [auth AA], PRA [auth BA], PRB [auth DA], PS [auth AO], PSA [auth BA], PSB [auth DA], PT [auth B5], PTA [auth BA], PTB [auth DA], PU [auth BA], PUA [auth BA], PUB [auth DA], PV [auth BA], PVA [auth BH], PVB [auth DA], PW [auth BA], PWA [auth CA], PWB [auth DA], PX [auth BA], PXA [auth CA], PXB [auth DA], PY [auth BA], PYA [auth CA], PYB [auth DA], PZ [auth BA], PZA [auth CA], PZB [auth DA], QAA [auth BA], QAB [auth CA], QAC [auth DA], QBA [auth BA], QBB [auth CA], QBC [auth DA], QCA [auth BA], QCB [auth CA], QCC [auth DA], QD [auth AA], QDA [auth BA], QDB [auth CH], QDC [auth DA], QE [auth AA], QEA [auth BA], QEB [auth D0], QEC [auth DA], QF [auth AA], QFA [auth BA], QFB [auth DA], QFC [auth DA], QG [auth AA], QGA [auth BA], QGB [auth DA], QGC [auth DA], QH [auth AA], QHA [auth BA], QHB [auth DA], QHC [auth DA], QI [auth AA], QIA [auth BA], QIB [auth DA], QIC [auth DA], QJ [auth AA], QJA [auth BA], QJB [auth DA], QJC [auth DA], QK [auth AA], QKA [auth BA], QKB [auth DA], QKC [auth DA], QL [auth AA], QLA [auth BA], QLB [auth DA], QLC [auth DA], QM [auth AA], QMA [auth BA], QMB [auth DA], QMC [auth DA], QN [auth AA], QNA [auth BA], QNB [auth DA], QNC [auth DA], QO [auth AA], QOA [auth BA], QOB [auth DA], QOC [auth DF], QP [auth AA], QPA [auth BA], QPB [auth DA], QQ [auth AA], QQA [auth BA], QQB [auth DA], QR [auth AA], QRA [auth BA], QRB [auth DA], QS [auth AO], QSA [auth BA], QSB [auth DA], QT [auth B6], QTA [auth BA], QTB [auth DA], QU [auth BA], QUA [auth BA], QUB [auth DA], QV [auth BA], QVA [auth BH], QVB [auth DA], QW [auth BA], QWA [auth CA], QWB [auth DA], QX [auth BA], QXA [auth CA], QXB [auth DA], QY [auth BA], QYA [auth CA], QYB [auth DA], QZ [auth BA], QZA [auth CA], QZB [auth DA], RAA [auth BA], RAB [auth CA], RAC [auth DA], RBA [auth BA], RBB [auth CA], RBC [auth DA], RCA [auth BA], RCB [auth CA], RCC [auth DA], RD [auth AA], RDA [auth BA], RDB [auth CJ], RDC [auth DA], RE [auth AA], REA [auth BA], REB [auth D1], REC [auth DA], RF [auth AA], RFA [auth BA], RFB [auth DA], RFC [auth DA], RG [auth AA], RGA [auth BA], RGB [auth DA], RGC [auth DA], RH [auth AA], RHA [auth BA], RHB [auth DA], RHC [auth DA], RI [auth AA], RIA [auth BA], RIB [auth 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[auth AA], SDA [auth BA], SDB [auth CJ], SDC [auth DA], SE [auth AA], SEA [auth BA], SEB [auth D1], SEC [auth DA], SF [auth AA], SFA [auth BA], SFB [auth DA], SFC [auth DA], SG [auth AA], SGA [auth BA], SGB [auth DA], SGC [auth DA], SH [auth AA], SHA [auth BA], SHB [auth DA], SHC [auth DA], SI [auth AA], SIA [auth BA], SIB [auth DA], SIC [auth DA], SJ [auth AA], SJA [auth BA], SJB [auth DA], SJC [auth DA], SK [auth AA], SKA [auth BA], SKB [auth DA], SKC [auth DA], SL [auth AA], SLA [auth BA], SLB [auth DA], SLC [auth DA], SM [auth AA], SMA [auth BA], SMB [auth DA], SMC [auth DA], SN [auth AA], SNA [auth BA], SNB [auth DA], SNC [auth DA], SO [auth AA], SOA [auth BA], SOB [auth DA], SOC [auth DN], SP [auth AA], SPA [auth BA], SPB [auth DA], SQ [auth AA], SQA [auth BA], SQB [auth DA], SR [auth AA], SRA [auth BA], SRB [auth DA], SS [auth AQ], SSA [auth BA], SSB [auth DA], ST [auth BA], STA [auth BA], STB [auth DA], SU [auth BA], SUA [auth BA], SUB [auth DA], SV [auth BA], SVA [auth BH], SVB [auth DA], SW [auth BA], SWA [auth CA], SWB [auth DA], SX [auth BA], SXA [auth CA], SXB [auth DA], SY [auth BA], SYA [auth CA], SYB [auth DA], SZ [auth BA], SZA [auth CA], SZB [auth DA], TAA [auth BA], TAB [auth CA], TAC [auth DA], TBA [auth BA], TBB [auth CA], TBC [auth DA], TCA [auth BA], TCB [auth CA], TCC [auth DA], TD [auth AA], TDA [auth BA], TDB [auth CM], TDC [auth DA], TE [auth AA], TEA [auth BA], TEB [auth D2], TEC [auth DA], TF [auth AA], TFA [auth BA], TFB [auth DA], TFC [auth DA], TG [auth AA], TGA [auth BA], TGB [auth DA], TGC [auth DA], TH [auth AA], THA [auth BA], THB [auth DA], THC [auth DA], TI [auth AA], TIA [auth BA], TIB [auth DA], TIC [auth DA], TJ [auth AA], TJA [auth BA], TJB [auth DA], TJC [auth DA], TK [auth AA], TKA [auth BA], TKB [auth DA], TKC [auth DA], TL [auth AA], TLA [auth BA], TLB [auth DA], TLC [auth DA], TM [auth AA], TMA [auth BA], TMB [auth DA], TMC [auth DA], TN [auth AA], TNA [auth BA], TNB [auth DA], TNC [auth DB], TO [auth AA], TOA [auth BA], TOB [auth DA], TOC [auth DN], TP [auth AA], TPA [auth BA], TPB [auth DA], TQ [auth AA], TQA [auth BA], TQB [auth DA], TR [auth AA], TRA [auth BA], TRB [auth DA], TS [auth AQ], TSA [auth BA], TSB [auth DA], TT [auth BA], TTA [auth BA], TTB [auth DA], TU [auth BA], TUA [auth BA], TUB [auth DA], TV [auth BA], TVA [auth BN], TVB [auth DA], TW [auth BA], TWA [auth CA], TWB [auth DA], TX [auth BA], TXA [auth CA], TXB [auth DA], TY [auth BA], TYA [auth CA], TYB [auth DA], TZ [auth BA], TZA [auth CA], TZB [auth DA], UAA [auth BA], UAB [auth CA], UAC [auth DA], UBA [auth BA], UBB [auth CA], UBC [auth DA], UCA [auth BA], UCB [auth CA], UCC [auth DA], UD [auth AA], UDA [auth BA], UDB [auth CM], UDC [auth DA], UE [auth AA], UEA [auth BA], UEB [auth D3], UEC [auth DA], UF [auth AA], UFA [auth BA], UFB [auth DA], UFC [auth DA], UG [auth AA], UGA [auth BA], UGB [auth DA], UGC [auth DA], UH [auth AA], UHA [auth BA], UHB [auth DA], UHC [auth DA], UI [auth AA], UIA [auth BA], UIB [auth DA], UIC [auth DA], UJ [auth AA], UJA [auth BA], UJB [auth DA], UJC [auth DA], UK [auth AA], UKA [auth BA], UKB [auth DA], UKC [auth DA], UL [auth AA], ULA [auth BA], ULB [auth DA], ULC [auth DA], UM [auth AA], UMA [auth BA], UMB [auth DA], UMC [auth DA], UN [auth AA], UNA [auth BA], UNB [auth DA], UNC [auth DB], UO [auth AA], UOA [auth BA], UOB [auth DA], UOC [auth DO], UP [auth AA], UPA [auth BA], UPB [auth DA], UQ [auth AA], UQA [auth BA], UQB [auth DA], UR [auth AA], URA [auth BA], URB [auth DA], US [auth AQ], USA [auth BA], USB [auth DA], UT [auth BA], UTA [auth BA], UTB [auth DA], UU [auth BA], UUA [auth BA], UUB [auth DA], UV [auth BA], UVA [auth BO], UVB [auth DA], UW [auth BA], UWA [auth CA], UWB [auth DA], UX [auth BA], UXA [auth CA], UXB [auth DA], UY [auth BA], UYA [auth CA], UYB [auth DA], UZ [auth BA], UZA [auth CA], UZB [auth DA], VAA [auth BA], VAB [auth CA], VAC [auth DA], VBA [auth BA], VBB [auth CA], VBC [auth DA], VCA [auth BA], VCB [auth CA], VCC [auth DA], VD [auth AA], 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[auth DA], WOC [auth DP], WP [auth AA], WPA [auth BA], WPB [auth DA], WQ [auth AA], WQA [auth BA], WQB [auth DA], WR [auth AC], WRA [auth BA], WRB [auth DA], WS [auth AV], WSA [auth BA], WSB [auth DA], WT [auth BA], WTA [auth BA], WTB [auth DA], WU [auth BA], WUA [auth BA], WUB [auth DA], WV [auth BA], WVA [auth BP], WVB [auth DA], WW [auth BA], WWA [auth CA], WWB [auth DA], WX [auth BA], WXA [auth CA], WXB [auth DA], WY [auth BA], WYA [auth CA], WYB [auth DA], WZ [auth BA], WZA [auth CA], WZB [auth DA], XAA [auth BA], XAB [auth CA], XAC [auth DA], XBA [auth BA], XBB [auth CA], XBC [auth DA], XCA [auth BA], XCB [auth CA], XCC [auth DA], XD [auth AA], XDA [auth BA], XDB [auth CQ], XDC [auth DA], XE [auth AA], XEA [auth BA], XEB [auth D5], XEC [auth DA], XF [auth AA], XFA [auth BA], XFB [auth DA], XFC [auth DA], XG [auth AA], XGA [auth BA], XGB [auth DA], XGC [auth DA], XH [auth AA], XHA [auth BA], XHB [auth DA], XHC [auth DA], XI [auth AA], XIA [auth BA], XIB [auth DA], XIC [auth DA], 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CA], YWB [auth DA], YX [auth BA], YXA [auth CA], YXB [auth DA], YY [auth BA], YYA [auth CA], YYB [auth DA], YZ [auth BA], YZA [auth CA], YZB [auth DA], ZAA [auth BA], ZAB [auth CA], ZAC [auth DA], ZBA [auth BA], ZBB [auth CA], ZBC [auth DA], ZCA [auth BA], ZCB [auth CA], ZCC [auth DA], ZD [auth AA], ZDA [auth BA], ZDB [auth CS], ZDC [auth DA], ZE [auth AA], ZEA [auth BA], ZEB [auth D6], ZEC [auth DA], ZF [auth AA], ZFA [auth BA], ZFB [auth DA], ZFC [auth DA], ZG [auth AA], ZGA [auth BA], ZGB [auth DA], ZGC [auth DA], ZH [auth AA], ZHA [auth BA], ZHB [auth DA], ZHC [auth DA], ZI [auth AA], ZIA [auth BA], ZIB [auth DA], ZIC [auth DA], ZJ [auth AA], ZJA [auth BA], ZJB [auth DA], ZJC [auth DA], ZK [auth AA], ZKA [auth BA], ZKB [auth DA], ZKC [auth DA], ZL [auth AA], ZLA [auth BA], ZLB [auth DA], ZLC [auth DA], ZM [auth AA], ZMA [auth BA], ZMB [auth DA], ZMC [auth DA], ZN [auth AA], ZNA [auth BA], ZNB [auth DA], ZNC [auth DB], ZO [auth AA], ZOA [auth BA], ZOB [auth DA], ZOC [auth DP], ZP [auth AA], ZPA [auth BA], ZPB [auth DA], ZQ [auth AA], ZQA [auth BA], ZQB [auth DA], ZR [auth AD], ZRA [auth BA], ZRB [auth DA], ZS [auth AV], ZSA [auth BA], ZSB [auth DA], ZT [auth BA], ZTA [auth BA], ZTB [auth DA], ZU [auth BA], ZUA [auth BB], ZUB [auth DA], ZV [auth BA], ZVA [auth BQ], ZVB [auth DA], ZW [auth BA], ZWA [auth CA], ZWB [auth DA], ZX [auth BA], ZXA [auth CA], ZXB [auth DA], ZY [auth BA], ZYA [auth CA], ZYB [auth DA], ZZ [auth BA], ZZA [auth CA], ZZB [auth DA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.041	α = 90
b = 453.514	β = 90
c = 616.103	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Ng, C.L., Lang, K., Meenan, N.A.G., Sharma, A., Kelley, A.C., Kleanthous, C., Ramakrishnan, V.
• This entry supersedes: 2XFZ, 2XG0, 2XG1, 2XG2

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2018-03-07
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2019-07-31
  Changes: Advisory, Data collection, Derived calculations