› 4v4t

X-ray diffraction
6.46Å resolution

Crystal structure of the whole ribosomal complex with a stop codon in the A-site.

Released:
DOI: 10.2210/pdb4v4t/pdb
PDB entry 4v4t coloured by chain, front view.
PDB entry 4v4t coloured by chain, side view.
PDB entry 4v4t coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.
Petry S, Brodersen DE, Murphy FV, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V
Cell 123 1255-66 (2005)
PMID: 16377566

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-135843 (preferred)
Entry contents:
49 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (55 distinct):
Small ribosomal subunit protein uS2 Chain: AB
Molecule details ›
Chain: AB
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 Chain: AC
Molecule details ›
Chain: AC
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 Chain: AD
Molecule details ›
Chain: AD
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 Chain: AE
Molecule details ›
Chain: AE
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 Chain: AF
Molecule details ›
Chain: AF
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 Chain: AG
Molecule details ›
Chain: AG
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
Small ribosomal subunit protein uS8 Chain: AH
Molecule details ›
Chain: AH
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: AI
Molecule details ›
Chain: AI
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 Chain: AJ
Molecule details ›
Chain: AJ
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 Chain: AK
Molecule details ›
Chain: AK
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 Chain: AL
Molecule details ›
Chain: AL
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 Chain: AM
Molecule details ›
Chain: AM
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
Small ribosomal subunit protein uS14 Chain: AN
Molecule details ›
Chain: AN
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY6 (Residues: 1-61; Coverage: 100%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: AO
Molecule details ›
Chain: AO
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 Chain: AP
Molecule details ›
Chain: AP
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
Small ribosomal subunit protein uS17 Chain: AQ
Molecule details ›
Chain: AQ
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: AR
Molecule details ›
Chain: AR
Length: 88 amino acids
Theoretical weight: 10.24 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 Chain: AS
Molecule details ›
Chain: AS
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 Chain: AT
Molecule details ›
Chain: AT
Length: 106 amino acids
Theoretical weight: 11.72 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 Chain: AU
Molecule details ›
Chain: AU
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
Large ribosomal subunit protein uL2 Chain: BD
Molecule details ›
Chain: BD
Length: 173 amino acids
Theoretical weight: 18.65 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5L3Z4 (Residues: 61-233; Coverage: 63%)
Gene names: GK0109, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: BE
Molecule details ›
Chain: BE
Length: 338 amino acids
Theoretical weight: 37.41 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P20279 (Residues: 2-312, 313-338; Coverage: 100%)
Gene names: rpl3, rrnAC1611
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: BF
Molecule details ›
Chain: BF
Length: 246 amino acids
Theoretical weight: 26.44 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P12735 (Residues: 1-246; Coverage: 100%)
Gene names: rpl4, rrnAC1610
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: BG
Molecule details ›
Chain: BG
Length: 176 amino acids
Theoretical weight: 19.42 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P14124 (Residues: 2-177; Coverage: 99%)
Gene names: rpl5, rrnAC1598
Sequence domains:
Large ribosomal subunit protein uL6 Chain: BH
Molecule details ›
Chain: BH
Length: 177 amino acids
Theoretical weight: 19.2 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5L408 (Residues: 2-178; Coverage: 99%)
Gene names: GK0121, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: BI
Molecule details ›
Chain: BI
Length: 149 amino acids
Theoretical weight: 16.34 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P02417 (Residues: 1-149; Coverage: 100%)
Gene name: rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chain: BN
Molecule details ›
Chain: BN
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P29198 (Residues: 1-145; Coverage: 100%)
Gene names: rpl13, rrnAC0065
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: BO
Molecule details ›
Chain: BO
Length: 122 amino acids
Theoretical weight: 13.37 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5L413 (Residues: 1-122; Coverage: 100%)
Gene names: GK0116, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: BP
Molecule details ›
Chain: BP
Length: 164 amino acids
Theoretical weight: 17.87 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P12737 (Residues: 2-165; Coverage: 99%)
Gene names: rpl15, rrnAC1590
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chain: BQ
Molecule details ›
Chain: BQ
Length: 138 amino acids
Theoretical weight: 15.31 KDa
Source organism: Thermus thermophilus
Large ribosomal subunit protein uL18 Chain: BS
Molecule details ›
Chain: BS
Length: 186 amino acids
Theoretical weight: 20.51 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P14123 (Residues: 2-187; Coverage: 100%)
Gene names: rpl18, rrnAC1593
Sequence domains: Ribosomal large subunit proteins 60S L5, and 50S L18
Large ribosomal subunit protein eL24 Chain: BT
Molecule details ›
Chain: BT
Length: 66 amino acids
Theoretical weight: 7.23 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P14116 (Residues: 2-67; Coverage: 99%)
Gene names: rpl24e, rrnAC0104
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL22 Chain: BW
Molecule details ›
Chain: BW
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: BX
Molecule details ›
Chain: BX
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P12732 (Residues: 2-85; Coverage: 99%)
Gene names: rpl23, rrnAC1609
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: BY
Molecule details ›
Chain: BY
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P10972 (Residues: 2-120; Coverage: 99%)
Gene names: rpl24, rrnAC1601
Sequence domains:
Large ribosomal subunit protein bL25 Chain: BZ
Molecule details ›
Chain: BZ
Length: 253 amino acids
Theoretical weight: 27 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RX88 (Residues: 1-237; Coverage: 100%)
Gene names: DR_0427, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL17 Chain: BR
Molecule details ›
Chain: BR
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein bL20 Chain: BU
Molecule details ›
Chain: BU
Length: 118 amino acids
Theoretical weight: 13.99 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RSW7 (Residues: 1-118; Coverage: 100%)
Gene names: DR_2004, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: BV
Molecule details ›
Chain: BV
Length: 100 amino acids
Theoretical weight: 11.17 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RY64 (Residues: 1-100; Coverage: 100%)
Gene names: DR_0086, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL29 Chain: B2
Molecule details ›
Chain: B2
Length: 70 amino acids
Theoretical weight: 7.76 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P10971 (Residues: 2-71; Coverage: 99%)
Gene names: rpl29, rrnAC1604
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: B3
Molecule details ›
Chain: B3
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL27 Chain: B0
Molecule details ›
Chain: B0
Length: 91 amino acids
Theoretical weight: 9.61 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RY65 (Residues: 1-91; Coverage: 100%)
Gene names: DR_0085, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL31 Chain: B4
Molecule details ›
Chain: B4
Length: 73 amino acids
Theoretical weight: 8.6 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RW44 (Residues: 1-73; Coverage: 100%)
Gene names: DR_0825, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: B5
Molecule details ›
Chain: B5
Length: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P49228 (Residues: 1-60; Coverage: 100%)
Gene names: DR_2366, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: B6
Molecule details ›
Chain: B6
Length: 82 amino acids
Theoretical weight: 9.29 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RSS4 (Residues: 1-55; Coverage: 100%)
Gene names: DR_2049, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: B7
Molecule details ›
Chain: B7
Length: 47 amino acids
Theoretical weight: 5.63 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RSH2 (Residues: 1-47; Coverage: 100%)
Gene names: DR_2152, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: B8
Molecule details ›
Chain: B8
Length: 64 amino acids
Theoretical weight: 7.26 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RSW6 (Residues: 1-64; Coverage: 97%)
Gene names: DR_2005, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: B9
Molecule details ›
Chain: B9
Length: 36 amino acids
Theoretical weight: 4.27 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9RSK0 (Residues: 1-36; Coverage: 97%)
Gene names: DR_2124, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL11 Chain: BK
Molecule details ›
Chain: BK
Length: 141 amino acids
Theoretical weight: 15.11 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P29395 (Residues: 1-141; Coverage: 100%)
Gene names: TM_0454, rplK
Sequence domains:
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1522 nucleotides
Theoretical weight: 493.96 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site tRNA (Phe) Chain: AV
Molecule details ›
Chain: AV
Length: 76 nucleotides
Theoretical weight: 24.52 KDa
Sequence domains: tRNA
E-site tRNA (Phe) Chain: AW
Molecule details ›
Chain: AW
Length: 76 nucleotides
Theoretical weight: 24.74 KDa
Sequence domains: tRNA
5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3' Chain: AX
Molecule details ›
Chain: AX
Length: 18 nucleotides
Theoretical weight: 5.7 KDa
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 123 nucleotides
Theoretical weight: 39.85 KDa
Sequence domains: 5S ribosomal RNA
23S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 2916 nucleotides
Theoretical weight: 948.28 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

No bound ligands
2 modified residues:
Ligand YYG 1 x YYG
Ligand PSU 2 x PSU

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P43212
Unit cell:
a: 517.414Å b: 517.414Å c: 365.385Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.356 0.354 0.361

Quick links

Citations

34 review citations

What recent ribosome structures have revealed about the mechanism of translation.
Schmeing et al. (2009)
33 more

1 mention without citation

Repurposing tRNAs for nonsense suppression.
Albers et al. (2021)