4WQU | pdb_00004wqu

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G trapped by the antibiotic dityromycin

• PDB DOI: https://doi.org/10.2210/pdb4WQU/pdb
• NAKB: 4WQU

• Classification: Ribosome/antibiotic
• Organism(s): Thermus thermophilus HB8, synthetic construct, Escherichia coli str. K-12 substr. MC4100, Streptomyces sp.
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-22 Released: 2015-01-28 
• Deposition Author(s): Lin, J., Gagnon, M.G., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.

Lin, J., Gagnon, M.G., Bulkley, D., Steitz, T.A.

(2015) Cell 160: 219-227

• PubMed: 25594181 
• DOI: https://doi.org/10.1016/j.cell.2014.11.049
• Primary Citation Related Structures: 
  4WPO, 4WQF, 4WQU, 4WQY


• PubMed Abstract: 
  

  The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 53-mer - AA1AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 53-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 53-mer - AA1AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 53-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4,754.77 kDa 
• Atom Count: 310,038 
• Modeled Residue Count: 22,747 
• Deposited Residue Count: 23,918 
• Unique protein chains: 53
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	C [auth AC], JB [auth CC]	228	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	D [auth AD], KB [auth CD]	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	E [auth AE], LB [auth CE]	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	F [auth AF], MB [auth CF]	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	G [auth AG], NB [auth CG]	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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	H [auth AH], OB [auth CH]	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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	I [auth AK], PB [auth CK]	173	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q8VVE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8VVE3  Go to UniProtKB:  Q8VVE3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	J [auth AL], QB [auth CL]	147	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP6  Go to UniProtKB:  Q5SLP6

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	K [auth AN], RB [auth CN]	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: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	L [auth AO], SB [auth CO]	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: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	M [auth AP], TB [auth CP]	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: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	N [auth AQ], UB [auth CQ]	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: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	O [auth AR], VB [auth CR]	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: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	P [auth AS], WB [auth CS]	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: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	Q [auth AT], XB [auth CT]	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: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	R [auth AU], YB [auth CU]	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: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	S [auth AV], ZB [auth CV]	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: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	AC [auth CW], T [auth AW]	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: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	BC [auth CX], U [auth AX]	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: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	CC [auth CY], V [auth AY]	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: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	DC [auth CZ], W [auth AZ]	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: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	EC [auth C0], X [auth A0]	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: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	FC [auth C1], Y [auth A1]	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: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	GC [auth C2], Z [auth A2]	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: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	AA [auth A3], HC [auth C3]	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: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	BA [auth A4], IC [auth C4]	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: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	CA [auth A5], JC [auth C5]	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: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	DA [auth A6], KC [auth C6]	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: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	EA [auth A7], LC [auth C7]	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: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	FA [auth A8], MC [auth C8]	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: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	GA [auth A9], NC [auth C9]	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: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	IA [auth BB], PC [auth DB]	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: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	JA [auth BC], QC [auth DC]	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: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	KA [auth BD], RC [auth DD]	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: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	LA [auth BE], SC [auth DE]	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: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	MA [auth BF], TC [auth DF]	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: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	NA [auth BG], UC [auth DG]	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: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	OA [auth BH], VC [auth DH]	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: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	PA [auth BI], WC [auth DI]	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: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	QA [auth BJ], XC [auth DJ]	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: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	RA [auth BK], YC [auth DK]	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: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	SA [auth BL], ZC [auth DL]	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: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	AD [auth DM], TA [auth BM]	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: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	BD [auth DN], UA [auth BN]	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: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	CD [auth DO], VA [auth BO]	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: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	DD [auth DP], WA [auth BP]	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: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	ED [auth DQ], XA [auth BQ]	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: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	FD [auth DR], YA [auth BR]	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: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	GD [auth DS], ZA [auth BS]	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: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	AB [auth BT], HD [auth DT]	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: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	BB [auth BU], ID [auth DU]	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: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9,Elongation factor G	FB [auth BZ], MD [auth DZ]	758	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rplI, TTHA0242, fusA, fus, TTHA1695
UniProt
Find proteins for Q5SHN5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN5  Go to UniProtKB:  Q5SHN5
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ1  Go to UniProtKB:  Q5SLQ1
UniProt Groups	Q5SHN5Q5SLQ1

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
Dityromycin	GB [auth BX], ND [auth DX]	10	Streptomyces sp.	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S Ribosomal RNA	A [auth AA], HB [auth CA]	2,915	Thermus thermophilus HB8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S Ribosomal RNA	B [auth AB], IB [auth CB]	121	Thermus thermophilus HB8

Entity ID: 34
Molecule	Chains	Length	Organism	Image
16S Ribosomal RNA	HA [auth BA], OC [auth DA]	1,521	Thermus thermophilus HB8

Entity ID: 55
Molecule	Chains	Length	Organism	Image
mRNA	CB [auth BV], JD [auth DV]	18	synthetic construct

Entity ID: 56
Molecule	Chains	Length	Organism	Image
P-site tRNA	DB [auth BW], EB [auth BY], KD [auth DW], LD [auth DY]	76	Escherichia coli str. K-12 substr. MC4100

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	PEC [auth DZ], YVA [auth BZ]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SF4	BEC [auth DD], HVA [auth BD]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN	BXB [auth CY], CMA [auth AY], FXB [auth C4], HXB [auth C5], IEC [auth DN], IXB [auth C6], LXB [auth C9], MMA [auth A4], NMA [auth A5], PVA [auth BN], QMA [auth A6], XMA [auth A9]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
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PPA [auth BA], PPB [auth CA], PQ [auth AA], PQA [auth BA], PQB [auth CA], PR [auth AA], PRA [auth BA], PRB [auth CA], PS [auth AA], PSA [auth BA], PSB [auth CA], PT [auth AA], PTA [auth BA], PTB [auth CA], PU [auth AA], PUA [auth BA], PUB [auth CA], PV [auth AA], PVB [auth CB], PW [auth AA], PWA [auth CA], PWB [auth CO], PX [auth AA], PXA [auth CA], PXB [auth DA], PY [auth AA], PYA [auth CA], PYB [auth DA], PZ [auth AA], PZA [auth CA], PZB [auth DA], QAA [auth AA], QAB [auth CA], QAC [auth DA], QBA [auth AA], QBB [auth CA], QBC [auth DA], QCA [auth AA], QCB [auth CA], QCC [auth DA], QD [auth AA], QDA [auth AA], QDB [auth CA], QDC [auth DA], QE [auth AA], QEA [auth AA], QEB [auth CA], QF [auth AA], QFA [auth AA], QFB [auth CA], QG [auth AA], QGA [auth AA], QGB [auth CA], QH [auth AA], QHA [auth AA], QHB [auth CA], QI [auth AA], QIA [auth AA], QIB [auth CA], QJ [auth AA], QJA [auth AB], QJB [auth CA], QK [auth AA], QKA [auth AE], QKB [auth CA], QL [auth AA], QLA [auth AU], QLB [auth CA], QM [auth AA], QMB [auth CA], QN [auth AA], QNA [auth BA], QNB [auth CA], QO [auth AA], QOA [auth BA], QOB [auth CA], QP [auth AA], QPA [auth BA], QPB [auth CA], QQ [auth AA], QQA [auth BA], QQB [auth CA], QR [auth AA], QRA [auth BA], QRB [auth CA], QS [auth AA], QSA [auth BA], QSB [auth CA], QT [auth AA], QTA [auth BA], QTB [auth CA], QU [auth AA], QUA [auth BA], QUB [auth CA], QV [auth AA], QVA [auth BN], QVB [auth CB], QW [auth AA], QWA [auth CA], QWB [auth CP], QX [auth AA], QXA [auth CA], QXB [auth DA], QY [auth AA], QYA [auth CA], QYB [auth DA], QZ [auth AA], QZA [auth CA], QZB [auth DA], RAA [auth AA], RAB [auth CA], RAC [auth DA], RBA [auth AA], RBB [auth CA], RBC [auth DA], RCA [auth AA], RCB [auth CA], RCC [auth DA], RD [auth AA], RDA [auth AA], RDB [auth CA], RDC [auth DA], RE [auth AA], REA [auth AA], REB [auth CA], RF [auth AA], RFA [auth AA], RFB [auth CA], RG [auth AA], RGA [auth AA], RGB [auth CA], RH [auth AA], RHA [auth AA], RHB [auth CA], RI [auth AA], RIA [auth AA], RIB [auth CA], RJ [auth AA], RJA [auth AB], RJB [auth CA], RK [auth AA], RKA [auth AF], RKB [auth CA], RL [auth AA], RLA [auth AU], RLB [auth CA], RM [auth AA], RMA [auth A6], RMB [auth CA], RN [auth AA], RNA [auth BA], RNB [auth CA], RO [auth AA], ROA [auth BA], ROB [auth CA], RP [auth AA], RPA [auth BA], RPB [auth CA], RQ [auth AA], RQA [auth BA], RQB [auth CA], RR [auth AA], RRA [auth BA], RRB [auth CA], RS [auth AA], RSA [auth BA], RSB [auth CA], RT [auth AA], RTA [auth BA], RTB [auth CA], RU [auth AA], RUA [auth BA], RUB [auth CA], RV [auth AA], RVA [auth BN], RVB [auth CB], RW [auth AA], RWA [auth CA], RWB [auth CQ], RX [auth AA], RXA [auth CA], RXB [auth DA], RY [auth AA], RYA [auth CA], RYB [auth DA], RZ [auth AA], RZA [auth CA], RZB [auth DA], SAA [auth AA], SAB [auth CA], SAC [auth DA], SBA [auth AA], SBB [auth CA], SBC [auth DA], SCA [auth AA], SCB [auth CA], SCC [auth DA], SD [auth AA], SDA [auth AA], SDB [auth CA], SDC [auth DA], SE [auth AA], SEA [auth AA], SEB [auth CA], SF [auth AA], SFA [auth AA], SFB [auth CA], SG [auth AA], SGA [auth AA], SGB [auth CA], SH [auth AA], SHA [auth AA], SHB [auth CA], SI [auth AA], SIA [auth AA], SIB [auth CA], SJ [auth AA], SJA [auth AB], SJB [auth CA], SK [auth AA], SKA [auth AF], SKB [auth CA], SL [auth AA], SLA [auth AV], SLB [auth CA], SM [auth AA], SMA [auth A7], SMB [auth CA], SN [auth AA], SNA [auth BA], SNB [auth CA], SO [auth AA], SOA [auth BA], SOB [auth CA], SP [auth AA], SPA [auth BA], SPB [auth CA], SQ [auth AA], SQA [auth BA], SQB [auth CA], SR [auth AA], SRA [auth BA], SRB [auth CA], SS [auth AA], SSA [auth BA], SSB [auth CA], ST [auth AA], STA [auth BA], STB [auth CA], SU [auth AA], SUA [auth BA], SUB [auth CA], SV [auth AA], SVA [auth BS], SVB [auth CB], SW [auth AA], SWA [auth CA], SWB [auth CQ], SX [auth AA], SXA [auth CA], SXB [auth DA], SY [auth AA], SYA [auth CA], SYB [auth DA], SZ [auth AA], SZA [auth CA], SZB [auth DA], TAA [auth AA], TAB [auth CA], TAC [auth DA], TBA [auth AA], TBB [auth CA], TBC [auth DA], TCA [auth AA], TCB [auth CA], TCC [auth DA], TD [auth AA], TDA [auth AA], TDB [auth CA], TDC [auth DA], TE [auth AA], TEA [auth AA], TEB [auth CA], TF [auth AA], TFA [auth AA], TFB [auth CA], TG [auth AA], TGA [auth AA], TGB [auth CA], TH [auth AA], THA [auth AA], THB [auth CA], TI [auth AA], TIA [auth AA], TIB [auth CA], TJ [auth AA], TJA [auth AB], TJB [auth CA], TK [auth AA], TKA [auth AF], TKB [auth CA], TL [auth AA], TLA [auth AV], TLB [auth CA], TM [auth AA], TMA [auth A7], TMB [auth CA], TN [auth AA], TNA [auth BA], TNB [auth CA], TO [auth AA], TOA [auth BA], TOB [auth CA], TP [auth AA], TPA [auth BA], TPB [auth CA], TQ [auth AA], TQA [auth BA], TQB [auth CA], TR [auth AA], TRA [auth BA], TRB [auth CA], TS [auth AA], TSA [auth BA], TSB [auth CA], TT [auth AA], TTA [auth BA], TTB [auth CA], TU [auth AA], TUA [auth BA], TUB [auth CA], TV [auth AA], TVA [auth BT], TVB [auth CB], TW [auth AA], TWA [auth CA], TWB [auth CQ], TX [auth AA], TXA [auth CA], TXB [auth DA], TY [auth AA], TYA [auth CA], TYB [auth DA], TZ [auth AA], TZA [auth CA], TZB [auth DA], UAA [auth AA], UAB [auth CA], UAC [auth DA], UBA [auth AA], UBB [auth CA], UBC [auth DA], UCA [auth AA], UCB [auth CA], UCC [auth DA], UD [auth AA], UDA [auth AA], UDB [auth CA], UDC [auth DA], UE [auth AA], UEA [auth AA], UEB [auth CA], UF [auth AA], UFA [auth AA], UFB [auth CA], UG [auth AA], UGA [auth AA], UGB [auth CA], UH [auth AA], UHA [auth AA], UHB [auth CA], UI [auth AA], UIA [auth AA], UIB [auth CA], UJ [auth AA], UJA [auth AB], UJB [auth CA], UK [auth AA], UKA [auth AF], UKB [auth CA], UL [auth AA], ULA [auth AV], ULB [auth CA], UM [auth AA], UMA [auth A7], UMB [auth CA], UN [auth AA], UNA [auth BA], UNB [auth CA], UO [auth AA], UOA [auth BA], UOB [auth CA], UP [auth AA], UPA [auth BA], UPB [auth CA], UQ [auth AA], UQA [auth BA], UQB [auth CA], UR [auth AA], URA [auth BA], URB [auth CA], US [auth AA], USA [auth BA], USB [auth CA], UT [auth AA], UTA [auth BA], UTB [auth CA], UU [auth AA], UUA [auth BA], UUB [auth CA], UV [auth AA], UVA [auth BW], UVB [auth CB], UW [auth AA], UWA [auth CA], UWB [auth CQ], UX [auth AA], UXA [auth CA], UXB [auth DA], UY [auth AA], UYA [auth CA], UYB [auth DA], UZ [auth AA], UZA [auth CA], UZB [auth DA], VAA [auth AA], VAB [auth CA], VAC [auth DA], VBA [auth AA], VBB [auth CA], VBC [auth DA], VCA [auth AA], VCB [auth CA], VCC [auth DA], VD [auth AA], VDA [auth AA], VDB [auth CA], VDC [auth DA], VE [auth AA], VEA [auth AA], VEB [auth CA], VF [auth AA], VFA [auth AA], VFB [auth CA], VG [auth AA], VGA [auth AA], VGB [auth CA], VH [auth AA], VHA [auth AA], VHB [auth CA], VI [auth AA], VIA [auth AA], VIB [auth CA], VJ [auth AA], VJA [auth AB], VJB [auth CA], VK [auth AA], VKA [auth AF], VKB [auth CA], VL [auth AA], VLA [auth AV], VLB [auth CA], VM [auth AA], VMA [auth A7], VMB [auth CA], VN [auth AA], VNA [auth BA], VNB [auth CA], VO [auth AA], VOA [auth BA], VOB [auth CA], VP [auth AA], VPA [auth BA], VPB [auth CA], VQ [auth AA], VQA [auth BA], VQB [auth CA], VR [auth AA], VRA [auth BA], VRB [auth CA], VS [auth AA], VSA [auth BA], VSB [auth CA], VT [auth AA], VTA [auth BA], VTB [auth CA], VU [auth AA], VUA [auth BA], VUB [auth CA], VV [auth AA], VVA [auth BW], VVB [auth CB], VW [auth AA], VWA [auth CA], VWB [auth CR], VX [auth AA], VXA [auth CA], VXB [auth DA], VY [auth AA], VYA [auth CA], VYB [auth DA], VZ [auth AA], VZA [auth CA], VZB [auth DA], WAA [auth AA], WAB [auth CA], WAC [auth DA], WBA [auth AA], WBB [auth CA], WBC [auth DA], WCA [auth AA], WCB [auth CA], WCC [auth DA], WD [auth AA], WDA [auth AA], WDB [auth CA], WDC [auth DA], WE [auth AA], WEA [auth AA], WEB [auth CA], WF [auth AA], WFA [auth AA], WFB [auth CA], WG [auth AA], WGA [auth AA], WGB [auth CA], WH [auth AA], WHA [auth AA], WHB [auth CA], WI [auth AA], WIA [auth AA], WIB [auth CA], WJ [auth AA], WJA [auth AB], WJB [auth CA], WK [auth AA], WKA [auth AF], WKB [auth CA], WL [auth AA], WLA [auth AV], WLB [auth CA], WM [auth AA], WMA [auth A8], WMB [auth CA], WN [auth AA], WNA [auth BA], WNB [auth CA], WO [auth AA], WOA [auth BA], WOB [auth CA], WP [auth AA], WPA [auth BA], WPB [auth CA], WQ [auth AA], WQA [auth BA], WQB [auth CA], WR [auth AA], WRA [auth BA], WRB [auth CA], WS [auth AA], WSA [auth BA], WSB [auth CA], WT [auth AA], WTA [auth BA], WTB [auth CA], WU [auth AA], WUA [auth BA], WUB [auth CA], WV [auth AA], WVA [auth BW], WVB [auth CB], WW [auth AA], WWA [auth CA], WWB [auth CU], WX [auth AA], WXA [auth CA], WXB [auth DA], WY [auth AA], WYA [auth CA], WYB [auth DA], WZ [auth AA], WZA [auth CA], WZB [auth DA], XAA [auth AA], XAB [auth CA], XAC [auth DA], XBA [auth AA], XBB [auth CA], XBC [auth DA], XCA [auth AA], XCB [auth CA], XCC [auth DA], XD [auth AA], XDA [auth AA], XDB [auth CA], XDC [auth DA], XE [auth AA], XEA [auth AA], XEB [auth CA], XF [auth AA], XFA [auth AA], XFB [auth CA], XG [auth AA], XGA [auth AA], XGB [auth CA], XH [auth AA], XHA [auth AA], XHB [auth CA], XI [auth AA], XIA [auth AA], XIB [auth CA], XJ [auth AA], XJA [auth AB], XJB [auth CA], XK [auth AA], XKA [auth AF], XKB [auth CA], XL [auth AA], XLA [auth AV], XLB [auth CA], XM [auth AA], XMB [auth CA], XN [auth AA], XNA [auth BA], XNB [auth CA], XO [auth AA], XOA [auth BA], XOB [auth CA], XP [auth AA], XPA [auth BA], XPB [auth CA], XQ [auth AA], XQA [auth BA], XQB [auth CA], XR [auth AA], XRA [auth BA], XRB [auth CA], XS [auth AA], XSA [auth BA], XSB [auth CA], XT [auth AA], XTA [auth BA], XTB [auth CA], XU [auth AA], XUA [auth BA], XUB [auth CA], XV [auth AA], XVA [auth BZ], XVB [auth CB], XW [auth AA], XWA [auth CA], XWB [auth CV], XX [auth AA], XXA [auth CA], XXB [auth DA], XY [auth AA], XYA [auth CA], XYB [auth DA], XZ [auth AA], XZA [auth CA], XZB [auth DA], YAA [auth AA], YAB [auth CA], YAC [auth DA], YBA [auth AA], YBB [auth CA], YBC [auth DA], YCA [auth AA], YCB [auth CA], YCC [auth DA], YD [auth AA], YDA [auth AA], YDB [auth CA], YDC [auth DA], YE [auth AA], YEA [auth AA], YEB [auth CA], YF [auth AA], YFA [auth AA], YFB [auth CA], YG [auth AA], YGA [auth AA], YGB [auth CA], YH [auth AA], YHA [auth AA], YHB [auth CA], YI [auth AA], YIA [auth AA], YIB [auth CA], YJ [auth AA], YJA [auth AB], YJB [auth CA], YK [auth AA], YKA [auth AF], YKB [auth CA], YL [auth AA], YLA [auth AW], YLB [auth CA], YM [auth AA], YMA [auth A9], YMB [auth CA], YN [auth AA], YNA [auth BA], YNB [auth CA], YO [auth AA], YOA [auth BA], YOB [auth CA], YP [auth AA], YPA [auth BA], YPB [auth CA], YQ [auth AA], YQA [auth BA], YQB [auth CA], YR [auth AA], YRA [auth BA], YRB [auth CA], YS [auth AA], YSA [auth BA], YSB [auth CA], YT [auth AA], YTA [auth BA], YTB [auth CA], YU [auth AA], YUA [auth BA], YUB [auth CA], YV [auth AA], YVB [auth CB], YW [auth AA], YWA [auth CA], YWB [auth CV], YX [auth AA], YXA [auth CA], YXB [auth DA], YY [auth AA], YYA [auth CA], YYB [auth DA], YZ [auth AA], YZA [auth CA], YZB [auth DA], ZAA [auth AA], ZAB [auth CA], ZAC [auth DA], ZBA [auth AA], ZBB [auth CA], ZBC [auth DA], ZCA [auth AA], ZCB [auth CA], ZCC [auth DA], ZD [auth AA], ZDA [auth AA], ZDB [auth CA], ZDC [auth DA], ZE [auth AA], ZEA [auth AA], ZEB [auth CA], ZF [auth AA], ZFA [auth AA], ZFB [auth CA], ZG [auth AA], ZGA [auth AA], ZGB [auth CA], ZH [auth AA], ZHA [auth AA], ZHB [auth CA], ZI [auth AA], ZIA [auth AA], ZIB [auth CA], ZJ [auth AA], ZJA [auth AB], ZJB [auth CA], ZK [auth AA], ZKA [auth AG], ZKB [auth CA], ZL [auth AA], ZLA [auth AW], ZLB [auth CA], ZM [auth AA], ZMA [auth BA], ZMB [auth CA], ZN [auth AA], ZNA [auth BA], ZNB [auth CA], ZO [auth AA], ZOA [auth BA], ZOB [auth CA], ZP [auth AA], ZPA [auth BA], ZPB [auth CA], ZQ [auth AA], ZQA [auth BA], ZQB [auth CA], ZR [auth AA], ZRA [auth BA], ZRB [auth CA], ZS [auth AA], ZSA [auth BA], ZSB [auth CA], ZT [auth AA], ZTA [auth BA], ZTB [auth CA], ZU [auth AA], ZUA [auth BA], ZUB [auth CA], ZV [auth AA], ZVA [auth CA], ZVB [auth CB], ZW [auth AA], ZWA [auth CA], ZWB [auth CW], ZX [auth AA], ZXA [auth CA], ZXB [auth DA], ZY [auth AA], ZYA [auth CA], ZYB [auth DA], ZZ [auth AA], ZZA [auth CA], ZZB [auth DA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
004	GB [auth BX], ND [auth DX]	L-PEPTIDE LINKING	C8 H9 N O2		--
2QY	GB [auth BX], ND [auth DX]	PEPTIDE LINKING	C10 H11 N O3		--
2QZ	GB [auth BX], ND [auth DX]	L-PEPTIDE LINKING	C6 H13 N O3		THR
2R1	GB [auth BX], ND [auth DX]	PEPTIDE LINKING	C6 H9 N O4		--
2R3	GB [auth BX], ND [auth DX]	L-PEPTIDE LINKING	C10 H13 N O4		TYR
MVA	GB [auth BX], ND [auth DX]	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 58
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001218	GB [auth BX], ND [auth DX]	Dityromycin	Peptide-like / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.84	α = 90
b = 450.58	β = 90
c = 623.43	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Lin, J., Gagnon, M.G., Steitz, T.A.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-11-04
  Changes: Data collection
• Version 1.2: 2016-05-04
  Changes: Structure summary
• Version 2.0: 2019-07-03
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2019-07-10
  Changes: Advisory, Data collection, Derived calculations
• Version 2.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 3.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary