Brand  (β version)

PDB ID: 4V9R

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Ligands
Code Name Style Show Link
MG Magnesium ion PoSSuM
SF4 Iron/sulfur cluster PoSSuM
ZN Zinc ion PoSSuM
FME N-formylmethionine PoSSuM
K Potassium ion PoSSuM
Non-standard Residues
Code Name Show
2QZ N,N-dimethyl-L-threonine
004 (2s)-amino(phenyl)ethanoic acid
MVA N-methylvaline
2R1 (2e)-2-amino-4-hydroxy-3-[(2r)-oxiran-2-yl]but-2-enoic acid
2R3 (betar)-beta-hydroxy-O-methyl-L-tyrosine
2QY (2z)-3-(4-hydroxyphenyl)-2-(methylamino)prop-2-enoic acid
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 4V9R   PDBj   RCSB PDB   PDBe
Header : Ribosome/Antibiotic
Title : Crystal structure of antibiotic DITYROMYCIN bound to 70S ribosome
Release Data : 2014-07-09
Compound :
mol_id molecule chains
1 16S Ribosomal RNA AA,CA
mol_id molecule chains
2 30S Ribosomal Protein S2 AB,CB
mol_id molecule chains
3 30S Ribosomal Protein S3 AC,CC
mol_id molecule chains
4 30S Ribosomal Protein S4 AD,CD
mol_id molecule chains
5 30S Ribosomal Protein S5 AE,CE
mol_id molecule chains
6 30S Ribosomal Protein S6 AF,CF
mol_id molecule chains
7 30S Ribosomal Protein S7 AG,CG
mol_id molecule chains
8 30S Ribosomal Protein S8 AH,CH
mol_id molecule chains
9 30S Ribosomal Protein S9 AI,CI
mol_id molecule chains
10 30S Ribosomal Protein S10 AJ,CJ
mol_id molecule chains
11 30S Ribosomal Protein S11 AK,CK
mol_id molecule chains
12 30S Ribosomal Protein S12 AL,CL
mol_id molecule chains
13 30S Ribosomal Protein S13 AM,CM
mol_id molecule chains
14 30S Ribosomal Protein S14 AN,CN
mol_id molecule chains
15 30S Ribosomal Protein S15 AO,CO
mol_id molecule chains
16 30S Ribosomal Protein S16 AP,CP
mol_id molecule chains
17 30S Ribosomal Protein S17 AQ,CQ
mol_id molecule chains
18 30S Ribosomal Protein S18 AR,CR
mol_id molecule chains
19 30S Ribosomal Protein S19 AS,CS
mol_id molecule chains
20 30S Ribosomal Protein S20 AT,CT
mol_id molecule chains
21 30S Ribosomal Protein THX AU,CU
mol_id molecule chains
22 mRNA AV,CV
mol_id molecule chains
23 P-site tRNA AX,CX
mol_id molecule chains
24 Dityromycin AW,CW
mol_id molecule chains
25 23S Ribosomal RNA BA,DA
mol_id molecule chains
26 5S Ribosomal RNA BB,DB
mol_id molecule chains
27 50S Ribosomal Protein L2 BD,DD
mol_id molecule chains
28 50S Ribosomal Protein L3 BE,DE
mol_id molecule chains
29 50S Ribosomal Protein L4 BF,DF
mol_id molecule chains
30 50S Ribosomal Protein L5 BG,DG
mol_id molecule chains
31 50S Ribosomal Protein L6 BH,DH
mol_id molecule chains
32 50S Ribosomal Protein L9 BI,DI
mol_id molecule chains
33 50S Ribosomal Protein L13 BN,DN
mol_id molecule chains
34 50S Ribosomal Protein L14 BO,DO
mol_id molecule chains
35 50S Ribosomal Protein L15 BP,DP
mol_id molecule chains
36 50S Ribosomal Protein L16 BQ,DQ
mol_id molecule chains
37 50S Ribosomal Protein L17 BR,DR
mol_id molecule chains
38 50S Ribosomal Protein L18 BS,DS
mol_id molecule chains
39 50S Ribosomal Protein L19 BT,DT
mol_id molecule chains
40 50S Ribosomal Protein L20 BU,DU
mol_id molecule chains
41 50S Ribosomal Protein L21 BV,DV
mol_id molecule chains
42 50S Ribosomal Protein L22 BW,DW
mol_id molecule chains
43 50S Ribosomal Protein L23 BX,DX
mol_id molecule chains
44 50S Ribosomal Protein L24 BY,DY
mol_id molecule chains
45 50S Ribosomal Protein L25 BZ,DZ
mol_id molecule chains
46 50S Ribosomal Protein L27 B0,D0
mol_id molecule chains
47 50S Ribosomal Protein L28 B1,D1
mol_id molecule chains
48 50S Ribosomal Protein L29 B2,D2
mol_id molecule chains
49 50S Ribosomal Protein L30 B3,D3
mol_id molecule chains
50 50S Ribosomal Protein L31 B4,D4
mol_id molecule chains
51 50S Ribosomal Protein L32 B5,D5
mol_id molecule chains
52 50S Ribosomal Protein L33 B6,D6
mol_id molecule chains
53 50S Ribosomal Protein L34 B7,D7
mol_id molecule chains
54 50S Ribosomal Protein L35 B8,D8
mol_id molecule chains
55 50S Ribosomal Protein L36 B9,D9
Source :
mol_id organism_scientific
1 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
2 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
3 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
4 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
5 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
6 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
7 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
8 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
9 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
10 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
11 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
12 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
13 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
14 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
15 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
16 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
17 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
18 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
19 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
20 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
21 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
22
synthetic: yes
other_details: IDT-Synthesized 24nt M-F-Stop mRNA
mol_id organism_scientific
23 Escherichia coli  (taxid:562)
strain: MRE-600
mol_id organism_scientific
24 Streptomyces sp.  (taxid:1931)
synthetic: yes
mol_id organism_scientific
25 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
26 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
27 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
28 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
29 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
30 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
31 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
32 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
33 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
34 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
35 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
36 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
37 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
38 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
39 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
40 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
41 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
42 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
43 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
44 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
45 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
46 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
47 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
48 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
49 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
50 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
51 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
52 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
53 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
54 Thermus thermophilus  (taxid:274)
strain: HB8
mol_id organism_scientific
55 Thermus thermophilus  (taxid:274)
strain: HB8
Authors : Bulkley, D.P., Brandi, L., Polikanov, Y.S., Fabbretti, A., O'Connor, M., Gualerzi, C.O., Steitz, T.A.
Keywords : 70S, Ribosome, Dityromycin, GE82832, Ribosomal Protein S12, EF-G, Translocation, Dityromycin and GE82832 bind protein S12 and block EF-G catalyzed translocation, 30S subunit with bound mRNA, P-site tRNA, Ribosome-Antibiotic complex
Exp. method : X-RAY DIFFRACTION ( 3.0000 Å )
Citation :

The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.

Bulkley, D.,Brandi, L.,Polikanov, Y.S.  et al.
(2014)  Cell Rep  6 : 357 - 365

PubMed: 24412368
DOI: 10.1016/j.celrep.2013.12.024

Reaction

Chain : AB, CB
UniProt : P80371 (RS2_THET8)
Reaction : -
Chain : AC, CC
UniProt : P80372 (RS3_THET8)
Reaction : -
Chain : AD, CD
UniProt : P80373 (RS4_THET8)
Reaction : -
Cofactor: Evidence: Note:
[4Fe-4S] cluster ECO:0000269 | PubMed:11866529
ECO:0000269 | PubMed:25775268
ECO:0000269 | PubMed:26792896
Binds 1 zinc ion per subunit (PubMed:11866529). In a number of structures (e.g. 4Y4O, 5FDV) a 4Fe-4S cluster is seen in place of the zinc cofactor (PubMed:25775268, PubMed:26792896).
Chain : AE, CE
UniProt : Q5SHQ5 (RS5_THET8)
Reaction : -
Chain : AF, CF
UniProt : Q5SLP8 (RS6_THET8)
Reaction : -
Chain : AG, CG
UniProt : P17291 (RS7_THET8)
Reaction : -
Chain : AH, CH
UniProt : Q5SHQ2 (RS8_THET8)
Reaction : -
Chain : AI, CI
UniProt : P80374 (RS9_THET8)
Reaction : -
Chain : AJ, CJ
UniProt : Q5SHN7 (RS10_THET8)
Reaction : -
Chain : AK, CK
UniProt : P80376 (RS11_THET8)
Reaction : -
Chain : AL, CL
UniProt : Q5SHN3 (RS12_THET8)
Reaction : -
Chain : AM, CM
UniProt : P80377 (RS13_THET8)
Reaction : -
Chain : AN, CN
UniProt : Q5SHQ1 (RS14Z_THET8)
Reaction : -
Cofactor: Evidence: Note:
Zn(2+) ECO:0000269 | PubMed:11866529
ECO:0000269 | PubMed:9746356
Binds 1 zinc ion per subunit.
Chain : AO, CO
UniProt : Q5SJ76 (RS15_THET8)
Reaction : -
Chain : AP, CP
UniProt : Q5SJH3 (RS16_THET8)
Reaction : -
Chain : AQ, CQ
UniProt : Q5SHP7 (RS17_THET8)
Reaction : -
Chain : AR, CR
UniProt : Q5SLQ0 (RS18_THET8)
Reaction : -
Chain : AS, CS
UniProt : Q5SHP2 (RS19_THET8)
Reaction : -
Chain : AT, CT
UniProt : P80380 (RS20_THET8)
Reaction : -
Chain : AU, CU
UniProt : Q5SIH3 (RSHX_THET8)
Reaction : -
Chain : BD, DD
UniProt : P60405 (RL2_THET8)
Reaction : -
Chain : BE, DE
UniProt : Q5SHN8 (RL3_THET8)
Reaction : -
Chain : BF, DF
UniProt : Q5SHN9 (RL4_THET8)
Reaction : -
Chain : BG, DG
UniProt : Q5SHQ0 (RL5_THET8)
Reaction : -
Chain : BH, DH
UniProt : Q5SHQ3 (RL6_THET8)
Reaction : -
Chain : BI, DI
UniProt : Q5SLQ1 (RL9_THET8)
Reaction : -
Chain : BN, DN
UniProt : P60488 (RL13_THET8)
Reaction : -
Chain : BO, DO
UniProt : Q5SHP8 (RL14_THET8)
Reaction : -
Chain : BP, DP
UniProt : Q5SHQ7 (RL15_THET8)
Reaction : -
Chain : BQ, DQ
UniProt : P60489 (RL16_THET8)
Reaction : -
Chain : BR, DR
UniProt : Q9Z9H5 (RL17_THET8)
Reaction : -
Chain : BS, DS
UniProt : Q5SHQ4 (RL18_THET8)
Reaction : -
Chain : BT, DT
UniProt : P60490 (RL19_THET8)
Reaction : -
Chain : BU, DU
UniProt : P60491 (RL20_THET8)
Reaction : -
Chain : BV, DV
UniProt : P60492 (RL21_THET8)
Reaction : -
Chain : BW, DW
UniProt : Q5SHP3 (RL22_THET8)
Reaction : -
Chain : BX, DX
UniProt : Q5SHP0 (RL23_THET8)
Reaction : -
Chain : BY, DY
UniProt : Q5SHP9 (RL24_THET8)
Reaction : -
Chain : BZ, DZ
UniProt : Q5SHZ1 (RL25_THET8)
Reaction : -
Chain : B0, D0
UniProt : P60493 (RL27_THET8)
Reaction : -
Chain : B1, D1
UniProt : P60494 (RL28_THET8)
Reaction : -
Chain : B2, D2
UniProt : Q5SHP6 (RL29_THET8)
Reaction : -
Chain : B3, D3
UniProt : Q5SHQ6 (RL30_THET8)
Reaction : -
Chain : B4, D4
UniProt : Q5SJE1 (RL31_THET8)
Reaction : -
Cofactor: Evidence: Note:
Zn(2+) ECO:0000255 | HAMAP-Rule:MF_00501
Binds 1 zinc ion per subunit.
Chain : B5, D5
UniProt : P80339 (RL32_THET8)
Reaction : -
Chain : B6, D6
UniProt : P35871 (RL33_THET8)
Reaction : -
Chain : B7, D7
UniProt : P80340 (RL34_THET8)
Reaction : -
Chain : B8, D8
UniProt : Q5SKU1 (RL35_THET8)
Reaction : -
Chain : B9, D9
UniProt : Q5SHR2 (RL36_THET8)
Reaction : -
Cofactor: Evidence: Note:
Zn(2+) ECO:0000250 | UniProtKB:P80256
Binds 1 zinc ion per subunit.