› 4v42

X-ray diffraction
5.5Å resolution

Crystal structure of the ribosome at 5.5 A resolution.

Released:
DOI: 10.2210/pdb4v42/pdb
PDB entry 4v42 coloured by chain, front view.
PDB entry 4v42 coloured by chain, side view.
PDB entry 4v42 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of the ribosome at 5.5 A resolution.
Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF
Science 292 883-96 (2001)
PMID: 11283358

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 49-mer (preferred)
PDBe Complex ID:
PDB-CPX-215557 (preferred)
Entry contents:
41 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (47 distinct):
Small ribosomal subunit protein uS2 Chain: AE
Molecule details ›
Chain: AE
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: AF
Molecule details ›
Chain: AF
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: AG
Molecule details ›
Chain: AG
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: AH
Molecule details ›
Chain: AH
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: AI
Molecule details ›
Chain: AI
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: AJ
Molecule details ›
Chain: AJ
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus
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: AK
Molecule details ›
Chain: AK
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: AL
Molecule details ›
Chain: AL
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus
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: AM
Molecule details ›
Chain: AM
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: AN
Molecule details ›
Chain: AN
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: AO
Molecule details ›
Chain: AO
Length: 135 amino acids
Theoretical weight: 14.92 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: AP
Molecule details ›
Chain: AP
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus
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: AQ
Molecule details ›
Chain: AQ
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus
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: AR
Molecule details ›
Chain: AR
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: AS
Molecule details ›
Chain: AS
Length: 91 amino acids
Theoretical weight: 10.81 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-17, 18-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: AT
Molecule details ›
Chain: AT
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: AU
Molecule details ›
Chain: AU
Length: 88 amino acids
Theoretical weight: 10.24 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: AV
Molecule details ›
Chain: AV
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: AW
Molecule details ›
Chain: AW
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: AX
Molecule details ›
Chain: AX
Length: 26 amino acids
Theoretical weight: 3.22 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-27; Coverage: 96%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Large ribosomal subunit protein uL1 Chain: BC
Molecule details ›
Chain: BC
Length: 228 amino acids
Theoretical weight: 24.74 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLP7 (Residues: 2-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chain: BD
Molecule details ›
Chain: BD
Length: 178 amino acids
Theoretical weight: 19.28 KDa
Source organisms: UniProt:
  • Canonical: P04257 (Residues: 61-197; Coverage: 50%)
  • Canonical: P20276 (Residues: 163-203; Coverage: 17%)
Gene names: rpl2, rplB, rrnAC1608
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: P02391 (Residues: 2-178; Coverage: 99%)
Gene name: rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL12 Chains: BI, BJ
Molecule details ›
Chains: BI, BJ
Length: 128 amino acids
Theoretical weight: 13.48 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P29396 (Residues: 1-128; Coverage: 100%)
Gene names: TM_0457, rplL
Sequence domains:
Large ribosomal subunit protein bL9 Chain: BK
Molecule details ›
Chain: BK
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 uL11 Chain: BL
Molecule details ›
Chain: BL
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:
Large ribosomal subunit protein uL13 Chain: BM
Molecule details ›
Chain: BM
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: BN
Molecule details ›
Chain: BN
Length: 122 amino acids
Theoretical weight: 13.37 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P04450 (Residues: 1-122; Coverage: 100%)
Gene name: rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: BO
Molecule details ›
Chain: BO
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 L10e Chain: BP
Molecule details ›
Chain: BP
Length: 138 amino acids
Theoretical weight: 15.31 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: A0A0X1KGB2 (Residues: 9-167; Coverage: 83%)
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL18 Chain: BQ
Molecule details ›
Chain: BQ
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: BR
Molecule details ›
Chain: BR
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: BS
Molecule details ›
Chain: BS
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: BT
Molecule details ›
Chain: BT
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: BU
Molecule details ›
Chain: BU
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: BV
Molecule details ›
Chain: BV
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Thermus thermophilus
Large ribosomal subunit protein uL29 Chain: BW
Molecule details ›
Chain: BW
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: BX
Molecule details ›
Chain: BX
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
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1522 nucleotides
Theoretical weight: 493.96 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
TRNA(PHE) Chains: AB, AC
Molecule details ›
Chains: AB, AC
Length: 76 nucleotides
Theoretical weight: 24.89 KDa
Sequence domains: tRNA
TRNA(PHE) Chain: AD
Molecule details ›
Chain: AD
Length: 74 nucleotides
Theoretical weight: 23.73 KDa
Sequence domains: tRNA
A- AND P-SITE MESSENGER RNA CODONS Chain: A1
Molecule details ›
Chain: A1
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
23S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 2916 nucleotides
Theoretical weight: 948.28 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 123 nucleotides
Theoretical weight: 39.85 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
12 modified residues:
Ligand 2MG 2 x 2MG
Ligand H2U 6 x H2U
Ligand M2G 2 x M2G
Ligand OMC 2 x OMC
Ligand OMG 2 x OMG
Ligand YG 2 x YG
Ligand PSU 5 x PSU
Ligand 5MC 5 x 5MC
Ligand 7MG 2 x 7MG
Ligand 5MU 3 x 5MU
Ligand 1MA 2 x 1MA
Ligand 4SU 1 x 4SU

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: I422
Unit cell:
a: 507.2Å b: 507.2Å c: 803.66Å
α: 90° β: 90° γ: 90°

Quick links

Citations

231 review citations

The noncoding RNA revolution-trashing old rules to forge new ones.
Cech et al. (2014)
230 more

2 mentions without citation

Ribosome Mechanics Informs about Mechanism.
Zimmermann et al. (2016)
1 more