6GSJ

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAThr in the A-site

• PDB DOI: https://doi.org/10.2210/pdb6GSJ/pdb
• NAKB: 6GSJ

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8, Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-06-14 Released: 2018-07-04 
• Deposition Author(s): Rozov, A., Yusupov, M., Yusupova, G.
• Funding Organization(s): French National Research Agency, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.252 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria.

Rozov, A., Wolff, P., Grosjean, H., Yusupov, M., Yusupova, G., Westhof, E.

(2018) Nucleic Acids Res 46: 7425-7435

• PubMed: 29931292 
• DOI: https://doi.org/10.1093/nar/gky547
• Primary Citation of Related Structures:  
  6GSJ, 6GSK, 6GSL


• PubMed Abstract: 
  

  We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick G•C and miscoding G•U pairs at the first two positions of the codon-anticodon duplex in ribosome functional complexes. Within the tight decoding center, miscoding G•U pairs occur, in all combinations, with a non-wobble geometry structurally indistinguishable from classical coding Watson-Crick pairs at the same first two positions. The contacts with the ribosomal grip surrounding the decoding center are all quasi-identical, except in the crowded environment of the amino group of a guanosine at the second position; in which case a G in the codons may be preferred. In vivo experimental data show that the translational errors due to miscoding by G•U pairs at the first two positions are the most frequently encountered ones, especially at the second position and with a G on the codon. Such preferred miscodings involve a switch from an A-U to a G•U pair in the tRNA/mRNA complex and very rarely from a G = C to a G•U pair. It is concluded that the frequencies of such occurrences are only weakly affected by the codon/anticodon structures but depend mainly on the stability and lifetime of the complex, the modifications present in the anticodon loop, especially those at positions 34 and 37, in addition to the relative concentration of cognate/near-cognate tRNA species present in the cellular tRNA pool.

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Organizational Affiliation: 

Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 47-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 47-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 46-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 46-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4,511.21 kDa 
• Atom Count: 294,252 
• Modelled Residue Count: 20,506 
• Deposited Residue Count: 21,509 
• Unique protein chains: 47
• Unique nucleic acid chains: 8

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B [auth 1E], DB [auth 12]	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 2E], EB [auth 22]	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 3E], FB [auth 32]	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 4E], GB [auth 42]	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 5E], HB [auth 52]	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 6E], IB [auth 62]	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 7E], JB [auth 72]	138	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9  Go to UniProtKB:  P0DOY9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I [auth 8E], KB [auth 82]	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 1I], LB [auth 1A]	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 2I], MB [auth 2A]	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 3I], NB [auth 3A]	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 4I], OB [auth 4A]	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 5I], PB [auth 5A]	61	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6  Go to UniProtKB:  P0DOY6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O [auth 6I], QB [auth 6A]	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 7I], RB [auth 7A]	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 8I], SB [auth 8A]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7  Go to UniProtKB:  P0DOY7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R [auth 9I], TB [auth 9A]	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 AI], UB [auth AA]	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 BI], VB [auth BA]	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 1F], WB [auth 1B]	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: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	BA [auth 11], DC [auth 19]	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	CA [auth 21], EC [auth 29]	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	DA [auth 31], FC [auth 39]	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	EA [auth 41], GC [auth 49]	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	FA [auth 51], HC [auth 59]	180	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY8  Go to UniProtKB:  P0DOY8

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	GA [auth 61], IC [auth 69]	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	HA [auth 58], JC [auth 15]	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	IA [auth 68], KC [auth 25]	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	JA [auth 78], LC [auth 35]	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	KA [auth 88], MC [auth 45]	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	LA [auth 98], NC [auth 55]	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	MA [auth A8], OC [auth 65]	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	NA [auth B8], PC [auth 75]	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	OA [auth C8], QC [auth 85]	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	PA [auth D8], RC [auth 95]	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	QA [auth E8], SC [auth A5]	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	RA [auth F8], TC [auth B5]	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	SA [auth G8], UC [auth C5]	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	TA [auth H8], VC [auth D5]	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	UA [auth I8], WC [auth E5]	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	VA [auth J8], XC [auth F5]	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	WA [auth K8], YC [auth G5]	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	XA [auth L8], ZC [auth H5]	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	YA [auth M8]	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	AD [auth J5], ZA [auth N8]	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 L34	AB [auth P8], BD [auth L5]	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: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	BB [auth Q8], CD [auth M5]	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: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A [auth 13], CB [auth 1G]	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
tRNAThr	V [auth 1K], XB [auth 1L]	76	Escherichia coli K-12

Entity ID: 23
Molecule	Chains	Length	Organism	Image
tRNAfMet	W [auth 2K], YB [auth 2L]	77	Escherichia coli K-12

Entity ID: 24
Molecule	Chains	Length	Organism	Image
tRNAThr	X [auth 3K]	76	Escherichia coli K-12

Entity ID: 25
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	AC [auth 4L], Y [auth 4K]	27	Escherichia coli K-12

Entity ID: 26
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	BC [auth 14], Z [auth 1H]	2,917	Thermus thermophilus HB8

Entity ID: 27
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	AA [auth 16], CC [auth 1J]	122	Thermus thermophilus HB8

Entity ID: 55
Molecule	Chains	Length	Organism	Image
tRNAThr	ZB [auth 3L]	76	Escherichia coli K-12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	BL [auth 3E], UQA [auth 32]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN	GL [auth 5I], YQA [auth 5A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth 1H], AAB [auth 14], ABA [auth 1H], ABB [auth 14], ACA [auth 1H], ACB [auth 14], ADA [auth 1H], ADB [auth 14], AE [auth 13], AEA [auth 1H], AEB [auth 14], AF [auth 13], AFA [auth 1H], AFB [auth 14], AG [auth 13], AGA [auth 1H], AGB [auth 14], AH [auth 13], AHA [auth 1H], AHB [auth 14], AI [auth 13], AIA [auth 1H], AIB [auth 1J], AJ [auth 13], AJA [auth 1H], AK [auth 13], AKA [auth 11], AL [auth 3E], ALA [auth 1G], AM [auth 1H], AMA [auth 1G], AN [auth 1H], ANA [auth 1G], AO [auth 1H], AOA [auth 1G], AP [auth 1H], APA [auth 1G], AQ [auth 1H], AQA [auth 1G], AR [auth 1H], ARA [auth BA], AS [auth 1H], ASA [auth 14], AT [auth 1H], ATA [auth 14], AU [auth 1H], AUA [auth 14], AV [auth 1H], AVA [auth 14], AW [auth 1H], AWA [auth 14], AX [auth 1H], AXA [auth 14], AY [auth 1H], AYA [auth 14], AZ [auth 1H], AZA [auth 14], BAA [auth 1H], BAB [auth 14], BBA [auth 1H], BBB [auth 14], BCA [auth 1H], BCB [auth 14], BDA [auth 1H], BDB [auth 14], BE [auth 13], BEA [auth 1H], BEB [auth 14], 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1G], WO [auth 1H], WOA [auth 1G], WP [auth 1H], WPA [auth 1G], WQ [auth 1H], WQA [auth 2A], WR [auth 1H], WRA [auth 14], WS [auth 1H], WSA [auth 14], WT [auth 1H], WTA [auth 14], WU [auth 1H], WUA [auth 14], WV [auth 1H], WVA [auth 14], WW [auth 1H], WWA [auth 14], WX [auth 1H], WXA [auth 14], WY [auth 1H], WYA [auth 14], WZ [auth 1H], WZA [auth 14], XAA [auth 1H], XAB [auth 14], XBA [auth 1H], XBB [auth 14], XCA [auth 1H], XCB [auth 14], XD [auth 13], XDA [auth 1H], XDB [auth 14], XE [auth 13], XEA [auth 1H], XEB [auth 14], XF [auth 13], XFA [auth 1H], XFB [auth 14], XG [auth 13], XGA [auth 1H], XGB [auth 14], XH [auth 13], XHA [auth 1H], XHB [auth 14], XI [auth 13], XIA [auth 1H], XJ [auth 13], XJA [auth 16], XK [auth 13], XKA [auth 1G], XL [auth 1H], XLA [auth 1G], XM [auth 1H], XMA [auth 1G], XN [auth 1H], XNA [auth 1G], XO [auth 1H], XOA [auth 1G], XP [auth 1H], XPA [auth 1G], XQ [auth 1H], XQA [auth 4A], XR [auth 1H], XRA [auth 14], XS [auth 1H], XSA [auth 14], XT [auth 1H], XTA [auth 14], XU [auth 1H], XUA [auth 14], XV [auth 1H], XVA [auth 14], XW [auth 1H], XWA [auth 14], XX [auth 1H], XXA [auth 14], XY [auth 1H], XYA [auth 14], XZ [auth 1H], XZA [auth 14], YAA [auth 1H], YAB [auth 14], YBA [auth 1H], YBB [auth 14], YCA [auth 1H], YCB [auth 14], YD [auth 13], YDA [auth 1H], YDB [auth 14], YE [auth 13], YEA [auth 1H], YEB [auth 14], YF [auth 13], YFA [auth 1H], YFB [auth 14], YG [auth 13], YGA [auth 1H], YGB [auth 14], YH [auth 13], YHA [auth 1H], YHB [auth 14], YI [auth 13], YIA [auth 1H], YJ [auth 13], YJA [auth 16], YK [auth 13], YKA [auth 1G], YL [auth 1H], YLA [auth 1G], YM [auth 1H], YMA [auth 1G], YN [auth 1H], YNA [auth 1G], YO [auth 1H], YOA [auth 1G], YP [auth 1H], YPA [auth 1G], YQ [auth 1H], YR [auth 1H], YRA [auth 14], YS [auth 1H], YSA [auth 14], YT [auth 1H], YTA [auth 14], YU [auth 1H], YUA [auth 14], YV [auth 1H], YVA [auth 14], YW [auth 1H], YWA [auth 14], YX [auth 1H], YXA [auth 14], YY [auth 1H], YYA [auth 14], YZ [auth 1H], YZA [auth 14], ZAA [auth 1H], ZAB [auth 14], ZBA [auth 1H], ZBB [auth 14], ZCA [auth 1H], ZCB [auth 14], ZD [auth 13], ZDA [auth 1H], ZDB [auth 14], ZE [auth 13], ZEA [auth 1H], ZEB [auth 14], ZF [auth 13], ZFA [auth 1H], ZFB [auth 14], ZG [auth 13], ZGA [auth 1H], ZGB [auth 14], ZH [auth 13], ZHA [auth 1H], ZHB [auth 1J], ZI [auth 13], ZIA [auth 1H], ZJ [auth 13], ZJA [auth 16], ZK [auth 13], ZKA [auth 1G], ZL [auth 1H], ZLA [auth 1G], ZM [auth 1H], ZMA [auth 1G], ZN [auth 1H], ZNA [auth 1G], ZO [auth 1H], ZOA [auth 1G], ZP [auth 1H], ZPA [auth 1G], ZQ [auth 1H], ZQA [auth 9A], ZR [auth 1H], ZRA [auth 14], ZS [auth 1H], ZSA [auth 14], ZT [auth 1H], ZTA [auth 14], ZU [auth 1H], ZUA [auth 14], ZV [auth 1H], ZVA [auth 14], ZW [auth 1H], ZWA [auth 14], ZX [auth 1H], ZXA [auth 14], ZY [auth 1H], ZYA [auth 14], ZZ [auth 1H], ZZA [auth 14]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.252 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.41	α = 90
b = 449.24	β = 90
c = 618.4	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Rozov, A., Yusupov, M., Yusupova, G.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-15-CE11-0021-01
	France	DBF20160635745
French National Research Agency	France	ANR-10-LABX-0036_NETRNA
European Research Council		294312
	Russian Federation	Russian Government Program of Competitive Growth of Kazan Federal University

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2018-09-05
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description