› 4u20

X-ray diffraction
2.9Å resolution

Crystal structure of the E. coli ribosome bound to flopristin.

Released:
DOI: 10.2210/pdb4u20/pdb
Model geometry
Fit model/data
PDB entry 4u20 coloured by chain, front view.
PDB entry 4u20 coloured by chain, side view.
PDB entry 4u20 coloured by chain, top view.
Source organisms:
Primary publication:
Synergy of streptogramin antibiotics occurs independently of their effects on translation.
Noeske J, Huang J, Olivier NB, Giacobbe RA, Zambrowski M, Cate JH
Antimicrob Agents Chemother 58 5269-79 (2014)
PMID: 24957822

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero 53-mer (preferred)
hetero 52-mer
Assembly name:
PDBe Complex ID:
PDB-CPX-293367 (preferred)
Entry contents:
50 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (53 distinct):
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
Length: 218 amino acids
Theoretical weight: 24.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V0 (Residues: 9-226; Coverage: 91%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: 88%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, CD
Small ribosomal subunit protein uS5 Chains: AE, CE
Small ribosomal subunit protein bS6, non-modified isoform Chains: AF, CF
Small ribosomal subunit protein uS7 Chains: AG, CG
Small ribosomal subunit protein uS8 Chains: AH, CH
Small ribosomal subunit protein uS9 Chains: AI, CI
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Small ribosomal subunit protein uS11 Chains: AK, CK
Small ribosomal subunit protein uS12 Chains: AL, CL
Small ribosomal subunit protein uS13 Chains: AM, CM
Small ribosomal subunit protein uS14 Chains: AN, CN
Small ribosomal subunit protein uS15 Chains: AO, CO
Small ribosomal subunit protein bS16 Chains: AP, CP
Small ribosomal subunit protein uS17 Chains: AQ, CQ
Small ribosomal subunit protein bS18 Chains: AR, CR
Small ribosomal subunit protein uS19 Chains: AS, CS
Small ribosomal subunit protein bS20 Chains: AT, CT
Small ribosomal subunit protein bS21 Chains: AU, CU
Large ribosomal subunit protein uL2 Chains: BC, DC
Large ribosomal subunit protein uL3 Chains: BD, DD
Large ribosomal subunit protein uL4 Chains: BE, DE
Large ribosomal subunit protein uL5 Chains: BF, DF
Large ribosomal subunit protein uL6 Chains: BG, DG
Large ribosomal subunit protein bL9 Chains: BH, DH
Large ribosomal subunit protein uL11 Chains: BI, DI
Large ribosomal subunit protein uL13 Chains: BJ, DJ
Large ribosomal subunit protein uL14 Chains: BK, DK
Large ribosomal subunit protein uL15 Chains: BL, DL
Large ribosomal subunit protein uL16 Chains: BM, DM
Large ribosomal subunit protein bL17 Chains: BN, DN
Large ribosomal subunit protein uL18 Chains: BO, DO
Large ribosomal subunit protein bL19 Chains: BP, DP
Large ribosomal subunit protein bL20 Chains: BQ, DQ
Large ribosomal subunit protein bL21 Chains: BR, DR
Large ribosomal subunit protein uL22 Chains: BS, DS
Large ribosomal subunit protein uL23 Chains: BT, DT
Large ribosomal subunit protein uL24 Chains: BU, DU
Large ribosomal subunit protein bL25 Chains: BV, DV
Large ribosomal subunit protein bL27 Chains: BW, DW
Large ribosomal subunit protein bL28 Chains: BX, DX
Large ribosomal subunit protein uL29 Chains: BY, DY
Large ribosomal subunit protein uL30 Chains: BZ, DZ
Large ribosomal subunit protein bL32 Chains: B0, D0
Large ribosomal subunit protein bL33 Chains: B1, D1
Large ribosomal subunit protein bL34 Chains: B2, D2
Large ribosomal subunit protein bL35 Chains: B3, D3
Large ribosomal subunit protein bL36A Chains: B4, D4
Large ribosomal subunit protein uL1 Chain: B5
16S ribosomal RNA Chains: AA, CA
23S ribosomal RNA Chains: BA, DA
5S ribosomal RNA Chains: BB, DB

Ligands and Environments

3 bound ligands:
Ligand MG 498 x MG
Ligand VIF 2 x VIF
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 211.79Å b: 433.06Å c: 623.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.235 0.278

Quick links

Citations

13 review citations

Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.
Lin et al. (2018)
12 more

2 mentions without citation

Mg2+ ions: do they bind to nucleobase nitrogens?
Leonarski et al. (2017)
1 more