4U25 image
Deposition Date 2014-07-16
Release Date 2014-07-30
Last Version Date 2024-10-23
Entry Detail
PDB ID:
4U25
Keywords:
Title:
Crystal structure of the E. coli ribosome bound to virginiamycin M1.
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: AA), BB (auth: CA)
Chain Length:1539
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), CB
Chain Length:218
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), DB (auth: CC)
Chain Length:206
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), EB (auth: CD)
Chain Length:205
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), FB (auth: CE)
Chain Length:150
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), GB (auth: CF)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), HB (auth: CG)
Chain Length:151
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: AH), IB (auth: CH)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), JB (auth: CI)
Chain Length:127
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), KB (auth: CJ)
Chain Length:98
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), LB (auth: CK)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), MB (auth: CL)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), NB (auth: CM)
Chain Length:114
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N (auth: AN), OB (auth: CN)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), PB (auth: CO)
Chain Length:88
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), QB (auth: CP)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: AQ), RB (auth: CQ)
Chain Length:80
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), SB (auth: CR)
Chain Length:55
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), TB (auth: CS)
Chain Length:79
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), UB (auth: CT)
Chain Length:85
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), VB (auth: CU)
Chain Length:51
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:VA (auth: B0), WC (auth: D0)
Chain Length:56
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:WA (auth: B1), XC (auth: D1)
Chain Length:50
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:XA (auth: B2), YC (auth: D2)
Chain Length:46
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:YA (auth: B3), ZC (auth: D3)
Chain Length:64
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:ZA (auth: B4), AD (auth: D4)
Chain Length:38
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:AB (auth: B5)
Chain Length:228
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:V (auth: BA), WB (auth: DA)
Chain Length:2903
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:W (auth: BB), XB (auth: DB)
Chain Length:119
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:X (auth: BC), YB (auth: DC)
Chain Length:271
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:Y (auth: BD), ZB (auth: DD)
Chain Length:209
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:Z (auth: BE), AC (auth: DE)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:AA (auth: BF), BC (auth: DF)
Chain Length:177
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:BA (auth: BG), CC (auth: DG)
Chain Length:176
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:CA (auth: BH), DC (auth: DH)
Chain Length:149
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:DA (auth: BI), EC (auth: DI)
Chain Length:141
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:EA (auth: BJ), FC (auth: DJ)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:FA (auth: BK), GC (auth: DK)
Chain Length:122
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:GA (auth: BL), HC (auth: DL)
Chain Length:143
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:HA (auth: BM), IC (auth: DM)
Chain Length:136
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:IA (auth: BN), JC (auth: DN)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:JA (auth: BO), KC (auth: DO)
Chain Length:116
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:KA (auth: BP), LC (auth: DP)
Chain Length:114
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:LA (auth: BQ), MC (auth: DQ)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:MA (auth: BR), NC (auth: DR)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:NA (auth: BS), OC (auth: DS)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:OA (auth: BT), PC (auth: DT)
Chain Length:93
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:PA (auth: BU), QC (auth: DU)
Chain Length:102
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:QA (auth: BV), RC (auth: DV)
Chain Length:94
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:RA (auth: BW), SC (auth: DW)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:SA (auth: BX), TC (auth: DX)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:TA (auth: BY), UC (auth: DY)
Chain Length:63
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:UA (auth: BZ), VC (auth: DZ)
Chain Length:58
Number of Molecules:2
Biological Source:Escherichia coli
Primary Citation
Synergy of streptogramin antibiotics occurs independently of their effects on translation.
Antimicrob.Agents Chemother. 58 5269 5279 (2014)
PMID: 24957822 DOI: 10.1128/AAC.03389-14

Abstact

Streptogramin antibiotics are divided into types A and B, which in combination can act synergistically. We compared the molecular interactions of the streptogramin combinations Synercid (type A, dalfopristin; type B, quinupristin) and NXL 103 (type A, flopristin; type B, linopristin) with the Escherichia coli 70S ribosome by X-ray crystallography. We further analyzed the activity of the streptogramin components individually and in combination. The streptogramin A and B components in Synercid and NXL 103 exhibit synergistic antimicrobial activity against certain pathogenic bacteria. However, in transcription-coupled translation assays, only combinations that include dalfopristin, the streptogramin A component of Synercid, show synergy. Notably, the diethylaminoethylsulfonyl group in dalfopristin reduces its activity but is the basis for synergy in transcription-coupled translation assays before its rapid hydrolysis from the depsipeptide core. Replacement of the diethylaminoethylsulfonyl group in dalfopristin by a nonhydrolyzable group may therefore be beneficial for synergy. The absence of general streptogramin synergy in transcription-coupled translation assays suggests that the synergistic antimicrobial activity of streptogramins can occur independently of the effects of streptogramin on translation.

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