Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.

Polikanov, Y.S.; Starosta, A.L.; Juette, M.F.; Altman, R.B.; Terry, D.S.; Lu, W.; Burnett, B.J.; Dinos, G.; Reynolds, K.A.; Blanchard, S.C.; Steitz, T.A.; Wilson, D.N.

doi:10.2210/pdb5dox/pdb

Macromolecule Content

Total Structure Weight: 4381256.00
Atom Count: 286666
Residue Count: 21242
Unique protein chains: 49
Unique nucleic acid chains: 3

5DOX

Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution

DOI: 10.2210/pdb5DOX/pdb
Entry 5DOX supersedes 4Z3R
NDB: 5DOX

Classification: Ribosome/Antibiotic
Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Thermus aquaticus, Thermus thermophilus HB8

Deposited: 2015-09-11 Released: 2015-12-30
Deposition Author(s): Polikanov, Y.S., Starosta, A.L., Juette, M.F., Altman, R.B., Terry, D.S., Lu, W., Burnett, B.J., Dinos, G., Reynolds, K., Blanchard, S.C., Steitz, T.A., Wilson, D.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.1 Å
R-Value Free: 0.284
R-Value Work: 0.232

wwPDB Validation3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.

Polikanov, Y.S., Starosta, A.L., Juette, M.F., Altman, R.B., Terry, D.S., Lu, W., Burnett, B.J., Dinos, G., Reynolds, K.A., Blanchard, S.C., Steitz, T.A., Wilson, D.N.

(2015) Mol.Cell 58: 832-844

PubMed: 26028538 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.molcel.2015.04.014
Primary Citation of Related Structures:
5DOY, 4Z3S, 4Z3R, 4Z3Q

PubMed Abstract:

The increase in multi-drug-resistant bacteria is limiting the effectiveness of currently approved antibiotics, leading to a renewed interest in antibiotics with distinct chemical scaffolds. We have solved the structures of the Thermus thermophilus 70S ribosome with A-, P-, and E-site tRNAs bound and in complex with either the aminocyclitol-containing antibiotic hygromycin A (HygA) or the nucleoside antibiotic A201A. Both antibiotics bind at the peptidyl transferase center and sterically occlude the CCA-end of the A-tRNA from entering the A site of the peptidyl transferase center. Single-molecule Förster resonance energy transfer (smFRET) experiments reveal that HygA and A201A specifically interfere with full accommodation of the A-tRNA, leading to the presence of tRNA accommodation intermediates and thereby inhibiting peptide bond formation. Thus, our results provide not only insight into the mechanism of action of HygA and A201A, but also into the fundamental process of tRNA accommodation during protein synthesis.

Organizational Affiliation:

Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany.,Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece.,Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany. Electronic address: wilson@lmb.uni-muenchen.de.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: thomas.steitz@yale.edu.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Department of Chemistry, Portland State University, Portland, OR 97207, USA.,Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA.,Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA; Tri-Institutional Training Program in Chemical Biology, New York, NY 10065, USA. Electronic address: scb2005@med.cornell.edu.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2	1D, 2D	276	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60405
Protein Feature View Full Protein Feature View for P60405

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3	1E, 2E	206	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHN8
Protein Feature View Full Protein Feature View for Q5SHN8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4	1F, 2F	210	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHN9
Protein Feature View Full Protein Feature View for Q5SHN9

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5	1G, 2G	182	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHQ0
Protein Feature View Full Protein Feature View for Q5SHQ0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6	1H, 2H	180	Thermus aquaticus	Mutation(s): 0 Gene Names: rplF
Find proteins for A0A0M9ADP1 (Thermus aquaticus) Go to UniProtKB: A0A0M9ADP1
Protein Feature View Full Protein Feature View for A0A0M9ADP1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L9	1I, 2I	148	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SLQ1
Protein Feature View Full Protein Feature View for Q5SLQ1

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13	1N, 2N	140	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60488
Protein Feature View Full Protein Feature View for P60488

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14	1O, 2O	122	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP8
Protein Feature View Full Protein Feature View for Q5SHP8

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15	1P, 2P	150	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHQ7
Protein Feature View Full Protein Feature View for Q5SHQ7

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	1Q, 2Q	141	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60489
Protein Feature View Full Protein Feature View for P60489

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L17	1R, 2R	118	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q9Z9H5
Protein Feature View Full Protein Feature View for Q9Z9H5

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18	1S, 2S	112	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHQ4
Protein Feature View Full Protein Feature View for Q5SHQ4

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19	1T, 2T	146	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60490
Protein Feature View Full Protein Feature View for P60490

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L20	1U, 2U	118	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60491
Protein Feature View Full Protein Feature View for P60491

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L21	1V, 2V	101	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60492
Protein Feature View Full Protein Feature View for P60492

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22	1W, 2W	113	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP3
Protein Feature View Full Protein Feature View for Q5SHP3

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23	1X, 2X	96	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP0
Protein Feature View Full Protein Feature View for Q5SHP0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24	1Y, 2Y	110	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP9
Protein Feature View Full Protein Feature View for Q5SHP9

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L25	1Z, 2Z	206	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHZ1
Protein Feature View Full Protein Feature View for Q5SHZ1

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	10, 20	85	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60493
Protein Feature View Full Protein Feature View for P60493

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L28	11, 21	98	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P60494
Protein Feature View Full Protein Feature View for P60494

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29	12, 22	72	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP6
Protein Feature View Full Protein Feature View for Q5SHP6

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30	13, 23	60	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHQ6
Protein Feature View Full Protein Feature View for Q5SHQ6

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L31	14, 24	71	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SJE1
Protein Feature View Full Protein Feature View for Q5SJE1

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32	15, 25	60	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80339
Protein Feature View Full Protein Feature View for P80339

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L33	16, 26	54	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P35871
Protein Feature View Full Protein Feature View for P35871

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L34	17, 27	49	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80340
Protein Feature View Full Protein Feature View for P80340

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L35	18, 28	65	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SKU1
Protein Feature View Full Protein Feature View for Q5SKU1

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L36	19, 29	37	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpmJ
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHR2
Protein Feature View Full Protein Feature View for Q5SHR2

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2	1b, 2b	256	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80371
Protein Feature View Full Protein Feature View for P80371

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S3	1c, 2c	239	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80372
Protein Feature View Full Protein Feature View for P80372

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S4	1d, 2d	209	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80373
Protein Feature View Full Protein Feature View for P80373

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S5	1e, 2e	162	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHQ5
Protein Feature View Full Protein Feature View for Q5SHQ5

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S6	1f, 2f	101	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SLP8
Protein Feature View Full Protein Feature View for Q5SLP8

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S7	1g, 2g	156	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P17291
Protein Feature View Full Protein Feature View for P17291

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S8	1h, 2h	138	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P0DOY9
Protein Feature View Full Protein Feature View for P0DOY9

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S9	1i, 2i	128	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80374
Protein Feature View Full Protein Feature View for P80374

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S10	1j, 2j	105	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHN7
Protein Feature View Full Protein Feature View for Q5SHN7

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S11	1k, 2k	129	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80376
Protein Feature View Full Protein Feature View for P80376

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S12	1l, 2l	132	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHN3
Protein Feature View Full Protein Feature View for Q5SHN3

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S13	1m, 2m	126	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80377
Protein Feature View Full Protein Feature View for P80377

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S14 type Z	1n, 2n	61	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsZ (rpsN)
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P0DOY6
Protein Feature View Full Protein Feature View for P0DOY6

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S15	1o, 2o	89	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SJ76
Protein Feature View Full Protein Feature View for Q5SJ76

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S16	1p, 2p	88	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SJH3
Protein Feature View Full Protein Feature View for Q5SJH3

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S17	1q, 2q	105	Thermus aquaticus	Mutation(s): 0 Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus) Go to UniProtKB: A0A0N0BLS5
Protein Feature View Full Protein Feature View for A0A0N0BLS5

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S18	1r, 2r	88	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SLQ0
Protein Feature View Full Protein Feature View for Q5SLQ0

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S19	1s, 2s	93	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP2
Protein Feature View Full Protein Feature View for Q5SHP2

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S20	1t, 2t	106	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80380
Protein Feature View Full Protein Feature View for P80380

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein Thx	1u, 2u	27	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0 Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SIH3
Protein Feature View Full Protein Feature View for Q5SIH3

Entity ID: 1
Molecule	Chains	Length	Organism
23S Ribosomal RNA	1A,2A	2915	Thermus thermophilus HB8

Entity ID: 2
Molecule	Chains	Length	Organism
5S Ribosomal RNA	1B,2B	121	Thermus thermophilus HB8

Entity ID: 32
Molecule	Chains	Length	Organism
16S Ribosomal RNA	1a,2a	1521	Thermus thermophilus HB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
SF4 Query on SF4 Download SDF File Download CCD File	1d, 2d	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-VKOJMFJBAC		Ligand Interaction
ZN Query on ZN Download SDF File Download CCD File	14, 15, 16, 19, 1n, 1Y, 24, 25, 26, 29, 2n, 2Y	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
HGR Query on HGR Download SDF File Download CCD File	1A, 2A	Hygromycin A C₂₃ H₂₉ N O₁₂ LDTRVHIISSLXOQ-IIHALWDASA-N		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	10, 11, 13, 15, 17, 18, 19, 1a, 1A, 1b, 1B, 1d, 1D, 1e, 1E, 1f, 1F, 1G, 1g, 1h, 1H, 1k, 1l, 1N, 1o, 1P, 1Q, 1q, 1r, 1R, 1t, 1T, 1U, 1V, 1W, 1X, 1Z, 20, 28, 2a, 2A, 2B, 2D, 2e, 2E, 2F, 2h, 2I, 2k, 2l, 2N, 2O, 2P, 2Q, 2R, 2t, 2T, 2V, 2W, 2X, 2Y	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 13 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU Query on PSU	1a, 1A, 2a, 2A	RNA LINKING	C₉ H₁₃ N₂ O₉ P		U
5MC Query on 5MC	1A, 1a, 2A, 2a	RNA LINKING	C₁₀ H₁₆ N₃ O₈ P		C
M2G Query on M2G	1a, 2a	RNA LINKING	C₁₂ H₁₈ N₅ O₈ P		G
MA6 Query on MA6	1a, 2a	RNA LINKING	C₁₂ H₁₈ N₅ O₇ P		A
2MG Query on 2MG	1a, 2a	RNA LINKING	C₁₁ H₁₆ N₅ O₈ P		G
UR3 Query on UR3	1a, 2a	RNA LINKING	C₁₀ H₁₅ N₂ O₉ P		U
OMG Query on OMG	1A, 2A	RNA LINKING	C₁₁ H₁₆ N₅ O₈ P		G
7MG Query on 7MG	1a, 2a	RNA LINKING	C₁₁ H₁₈ N₅ O₈ P		G
5MU Query on 5MU	1A, 2A	RNA LINKING	C₁₀ H₁₅ N₂ O₉ P		U
2MA Query on 2MA	1A, 2A	RNA LINKING	C₁₁ H₁₆ N₅ O₇ P		A
2MU Query on 2MU	1A, 2A	RNA LINKING	C₁₁ H₁₇ N₂ O₉ P		U
0TD Query on 0TD	1l, 2l	L-PEPTIDE LINKING	C₅ H₉ N O₄ S		ASP
4OC Query on 4OC	1A, 1a, 2A, 2a	RNA LINKING	C₁₁ H₁₈ N₃ O₈ P		C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.1 Å
R-Value Free: 0.284
R-Value Work: 0.232
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 209.510	α = 90.00
b = 448.290	β = 90.00
c = 619.370	γ = 90.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2015-09-11
Released Date: 2015-12-30
Deposition Author(s): Polikanov, Y.S., Starosta, A.L., Juette, M.F., Altman, R.B., Terry, D.S., Lu, W., Burnett, B.J., Dinos, G., Reynolds, K., Blanchard, S.C., Steitz, T.A., Wilson, D.N.
This entry supersedes: 4Z3R

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095737
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM079238
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM098859
German Research Foundation (DFG)	Germany	FOR1805
German Research Foundation (DFG)	Germany	WI3285/3-1
German Research Foundation (DFG)	Germany	GRK1721

Revision History

Version 1.0: 2015-12-30
Type: Initial release
Version 1.1: 2016-09-14
Type: Derived calculations
Version 1.2: 2017-09-20
Type: Author supporting evidence, Derived calculations
Version 1.3: 2017-09-27
Type: Author supporting evidence
Version 1.4: 2019-12-25
Type: Author supporting evidence, Derived calculations

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

159670 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

5DOX

Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution

Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.

Entity ID: 3

Entity ID: 4

Entity ID: 5

Entity ID: 6

Entity ID: 7

Entity ID: 8

Entity ID: 9

Entity ID: 10

Entity ID: 11

Entity ID: 12

Entity ID: 13

Entity ID: 14

Entity ID: 15

Entity ID: 16

Entity ID: 17

Entity ID: 18

Entity ID: 19

Entity ID: 20

Entity ID: 21

Entity ID: 22

Entity ID: 23

Entity ID: 24

Entity ID: 25

Entity ID: 26

Entity ID: 27

Entity ID: 28

Entity ID: 29

Entity ID: 30

Entity ID: 31

Entity ID: 33

Entity ID: 34

Entity ID: 35

Entity ID: 36

Entity ID: 37

Entity ID: 38

Entity ID: 39

Entity ID: 40

Entity ID: 41

Entity ID: 42

Entity ID: 43

Entity ID: 44

Entity ID: 45

Entity ID: 46

Entity ID: 47

Entity ID: 48

Entity ID: 49

Entity ID: 50

Entity ID: 51

Entity ID: 52

Entity ID: 1

Entity ID: 2

Entity ID: 32

Experimental Data

Structure Validation

Deposition Data

Revision History