› 4v5k

X-ray diffraction
3.2Å resolution

Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome

Released:
DOI: 10.2210/pdb4v5k/pdb
Model geometry
Fit model/data
PDB entry 4v5k coloured by chain, front view.
PDB entry 4v5k coloured by chain, side view.
PDB entry 4v5k coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
Ng CL, Lang K, Meenan NA, Sharma A, Kelley AC, Kleanthous C, Ramakrishnan V
OpenAccess logo Nat Struct Mol Biol 17 1241-1246 (2010)
PMID: 20852642

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-293160 (preferred)
Entry contents:
52 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (58 distinct):
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, CD
Small ribosomal subunit protein uS5 Chains: AE, CE
Small ribosomal subunit protein bS6 Chains: AF, CF
Small ribosomal subunit protein uS7 Chains: AG, CG
30S RIBOSOMAL PROTEIN S8 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
30S RIBOSOMAL PROTEIN S14 TYPE Z Chains: AN, CN
Small ribosomal subunit protein uS15 Chains: AO, CO
Small ribosomal subunit protein bS16 Chains: AP, CP
30S RIBOSOMAL PROTEIN S17 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 bTHX Chains: AU, CU
Colicin E3 Chains: AY, CY
Large ribosomal subunit protein bL27 Chains: B0, D0
Large ribosomal subunit protein bL28 Chains: B1, D1
Large ribosomal subunit protein uL29 Chains: B2, D2
Large ribosomal subunit protein uL30 Chains: B3, D3
Large ribosomal subunit protein bL31 Chains: B4, D4
Large ribosomal subunit protein bL32 Chains: B5, D5
Large ribosomal subunit protein bL33 Chains: B6, D6
Large ribosomal subunit protein bL34 Chains: B7, D7
Large ribosomal subunit protein bL35 Chains: B8, D8
Large ribosomal subunit protein bL36 Chains: B9, D9
Large ribosomal subunit protein uL1 Chains: BC, DC
Large ribosomal subunit protein uL2 Chains: BD, DD
Large ribosomal subunit protein uL3 Chains: BE, DE
Large ribosomal subunit protein uL4 Chains: BF, DF
Large ribosomal subunit protein uL5 Chains: BG, DG
50S RIBOSOMAL PROTEIN L6 Chains: BH, DH
Large ribosomal subunit protein bL9 Chains: BI, DI
50S RIBOSOMAL PROTEIN L10 Chains: BJ, DJ
Large ribosomal subunit protein uL13 Chains: BN, DN
Large ribosomal subunit protein uL14 Chains: BO, DO
Large ribosomal subunit protein uL15 Chains: BP, DP
Large ribosomal subunit protein uL16 Chains: BQ, DQ
Large ribosomal subunit protein bL17 Chains: BR, DR
Large ribosomal subunit protein uL18 Chains: BS, DS
Large ribosomal subunit protein bL19 Chains: BT, DT
Large ribosomal subunit protein bL20 Chains: BU, DU
Large ribosomal subunit protein bL21 Chains: BV, DV
Large ribosomal subunit protein uL22 Chains: BW, DW
Large ribosomal subunit protein uL23 Chains: BX, DX
Large ribosomal subunit protein uL24 Chains: BY, DY
Large ribosomal subunit protein bL25 Chains: BZ, DZ
16S ribosomal RNA Chains: AA, CA
E-SITE TRNA PHE OR P-SITE TRNA PHE Chains: AV, AW, CV, CW
Messenger RNA Chain: AX
23S ribosomal RNA Chains: BA, DA
5S ribosomal RNA Chains: BB, DB
Messenger RNA Chain: CX

Ligands and Environments

2 bound ligands:
Ligand MG 2334 x MG
Ligand ZN 4 x ZN
1 modified residue:
Ligand A3P 2 x A3P

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 212.041Å b: 453.514Å c: 616.103Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.27
Expression system: Escherichia coli

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Citations

10 review citations

Aromatic rings in chemical and biological recognition: energetics and structures.
Salonen et al. (2011)
9 more

1 mention without citation

Genus for biomolecules.
Rubach et al. (2020)