› 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
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-132798 (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
Molecule details ›
Chains: AD, CD
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: AE, CE
Molecule details ›
Chains: AE, CE
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: AF, CF
Molecule details ›
Chains: AF, CF
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: AG, CG
Molecule details ›
Chains: AG, CG
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S RIBOSOMAL PROTEIN S8 Chains: AH, CH
Molecule details ›
Chains: AH, CH
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS9 Chains: AI, CI
Molecule details ›
Chains: AI, CI
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Molecule details ›
Chains: AJ, CJ
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: AK, CK
Molecule details ›
Chains: AK, CK
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: AL, CL
Molecule details ›
Chains: AL, CL
Length: 135 amino acids
Theoretical weight: 14.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: AM, CM
Molecule details ›
Chains: AM, CM
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S RIBOSOMAL PROTEIN S14 TYPE Z Chains: AN, CN
Molecule details ›
Chains: AN, CN
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS15 Chains: AO, CO
Molecule details ›
Chains: AO, CO
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: AP, CP
Molecule details ›
Chains: AP, CP
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S RIBOSOMAL PROTEIN S17 Chains: AQ, CQ
Molecule details ›
Chains: AQ, CQ
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein bS18 Chains: AR, CR
Molecule details ›
Chains: AR, CR
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: AS, CS
Molecule details ›
Chains: AS, CS
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: AT, CT
Molecule details ›
Chains: AT, CT
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: AU, CU
Molecule details ›
Chains: AU, CU
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Colicin E3 Chains: AY, CY
Molecule details ›
Chains: AY, CY
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00646 (Residues: 455-551; Coverage: 18%)
Gene names: ceaC, col
Sequence domains: Cytotoxic
Large ribosomal subunit protein bL27 Chains: B0, D0
Molecule details ›
Chains: B0, D0
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: B1, D1
Molecule details ›
Chains: B1, D1
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: B2, D2
Molecule details ›
Chains: B2, D2
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: B3, D3
Molecule details ›
Chains: B3, D3
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chains: B4, D4
Molecule details ›
Chains: B4, D4
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-71; Coverage: 100%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: B5, D5
Molecule details ›
Chains: B5, D5
Length: 60 amino acids
Theoretical weight: 6.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: B6, D6
Molecule details ›
Chains: B6, D6
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 1-54; Coverage: 100%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: B7, D7
Molecule details ›
Chains: B7, D7
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: B8, D8
Molecule details ›
Chains: B8, D8
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: B9, D9
Molecule details ›
Chains: B9, D9
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL1 Chains: BC, DC
Molecule details ›
Chains: BC, DC
Length: 229 amino acids
Theoretical weight: 24.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 1-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chains: BD, DD
Molecule details ›
Chains: BD, DD
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: BE, DE
Molecule details ›
Chains: BE, DE
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: BF, DF
Molecule details ›
Chains: BF, DF
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-210; Coverage: 100%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: BG, DG
Molecule details ›
Chains: BG, DG
Length: 182 amino acids
Theoretical weight: 21.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S RIBOSOMAL PROTEIN L6 Chains: BH, DH
Molecule details ›
Chains: BH, DH
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein bL9 Chains: BI, DI
Molecule details ›
Chains: BI, DI
Length: 148 amino acids
Theoretical weight: 16.42 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
50S RIBOSOMAL PROTEIN L10 Chains: BJ, DJ
Molecule details ›
Chains: BJ, DJ
Length: 131 amino acids
Theoretical weight: 11.17 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein uL13 Chains: BN, DN
Molecule details ›
Chains: BN, DN
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: BO, DO
Molecule details ›
Chains: BO, DO
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: BP, DP
Molecule details ›
Chains: BP, DP
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-150; Coverage: 100%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: BQ, DQ
Molecule details ›
Chains: BQ, DQ
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chains: BR, DR
Molecule details ›
Chains: BR, DR
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: BS, DS
Molecule details ›
Chains: BS, DS
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 1-112; Coverage: 100%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: BT, DT
Molecule details ›
Chains: BT, DT
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: BU, DU
Molecule details ›
Chains: BU, DU
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: BV, DV
Molecule details ›
Chains: BV, DV
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chains: BW, DW
Molecule details ›
Chains: BW, DW
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: BX, DX
Molecule details ›
Chains: BX, DX
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: BY, DY
Molecule details ›
Chains: BY, DY
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-110; Coverage: 100%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: BZ, DZ
Molecule details ›
Chains: BZ, DZ
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
16S ribosomal RNA Chains: AA, CA
Molecule details ›
Chains: AA, CA
Length: 1522 nucleotides
Theoretical weight: 494.04 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
E-SITE TRNA PHE OR P-SITE TRNA PHE Chains: AV, AW, CV, CW
Molecule details ›
Chains: AV, AW, CV, CW
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
Messenger RNA Chain: AX
Molecule details ›
Chain: AX
Length: 25 nucleotides
Theoretical weight: 8.16 KDa
23S ribosomal RNA Chains: BA, DA
Molecule details ›
Chains: BA, DA
Length: 2848 nucleotides
Theoretical weight: 926.37 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: BB, DB
Molecule details ›
Chains: BB, DB
Length: 122 nucleotides
Theoretical weight: 39.49 KDa
Sequence domains: 5S ribosomal RNA
Messenger RNA Chain: CX
Molecule details ›
Chain: CX
Length: 25 nucleotides
Theoretical weight: 8.2 KDa

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

Entry percentile scores
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

Quick links

Citations

10 review citations

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1 mention without citation

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