› 4v4r

X-ray diffraction
5.9Å resolution

Crystal structure of the whole ribosomal complex.

Released:
DOI: 10.2210/pdb4v4r/pdb
PDB 4v4r coloured by chain and viewed from the front.
PDB 4v4r coloured by chain and viewed from the side.
PDB 4v4r coloured by chain and viewed from the top.
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 56-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (56 distinct):
30S ribosomal protein S2 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
30S ribosomal protein S3 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:
30S ribosomal protein S4 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:
30S ribosomal protein S5 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:
30S ribosomal protein S6 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
30S ribosomal protein S7 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
30S ribosomal protein S8 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
30S ribosomal protein S9 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
30S ribosomal protein S10 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
30S ribosomal protein S11 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
30S ribosomal protein S12 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
30S ribosomal protein S13 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
30S ribosomal protein S14 type Z 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
30S ribosomal protein S15 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
30S ribosomal protein S16 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
30S ribosomal protein S17 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
30S ribosomal protein S18 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
30S ribosomal protein S19 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
30S ribosomal protein S20 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
30S ribosomal protein Thx 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
Peptide chain release factor 1 Chain: AY
Molecule details ›
Chain: AY
Length: 354 amino acids
Theoretical weight: 40.15 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: P96077 (Residues: 1-354; Coverage: 100%)
Gene names: TTHA1940, prfA
Sequence domains:
50S ribosomal protein L2 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
50S ribosomal protein L3 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
50S ribosomal protein L4 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
50S ribosomal protein L5 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:
50S ribosomal protein L6 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
50S ribosomal protein L9 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:
50S ribosomal protein L13 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
50S ribosomal protein L14 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
50S ribosomal protein L15 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
50S ribosomal protein L18 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
50S ribosomal protein L24e 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
50S ribosomal protein L22 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
50S ribosomal protein L23 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
50S ribosomal protein L24 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:
50S ribosomal protein L25 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:
50S ribosomal protein L17 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
50S ribosomal protein L20 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
50S ribosomal protein L21 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
50S ribosomal protein L29 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
50S ribosomal protein L30 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
50S ribosomal protein L27 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
50S ribosomal protein L31 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
50S ribosomal protein L32 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
50S ribosomal protein L33 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
50S ribosomal protein L34 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
50S ribosomal protein L35 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
50S ribosomal protein L36 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
50S ribosomal protein L11 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'-R(*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: 518.993Å b: 518.993Å c: 365.139Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.353 0.351 0.371
Expression system: Escherichia coli

Quick links

Citations

28 review citations

Engineered Ribosomes for Basic Science and Synthetic Biology.
d'Aquino et al. (2018)
27 more