› 4v42

X-ray diffraction
5.5Å resolution

Crystal structure of the ribosome at 5.5 A resolution.

Released:
DOI: 10.2210/pdb4v42/pdb
PDB 4v42 coloured by chain and viewed from the front.
PDB 4v42 coloured by chain and viewed from the side.
PDB 4v42 coloured by chain and viewed from the top.
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)
Entry contents:
41 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (47 distinct):
30S ribosomal protein S2 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
30S ribosomal protein S3 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:
30S ribosomal protein S4 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:
30S ribosomal protein S5 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:
30S ribosomal protein S6 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
30S ribosomal protein S7 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
30S ribosomal protein S8 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
30S ribosomal protein S9 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
30S ribosomal protein S10 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
30S ribosomal protein S11 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
30S ribosomal protein S12 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
30S ribosomal protein S13 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
30S ribosomal protein S14 type Z 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
30S ribosomal protein S15 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
30S ribosomal protein S16 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
30S ribosomal protein S17 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
30S ribosomal protein S18 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
30S ribosomal protein S19 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
30S ribosomal protein S20 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
30S ribosomal protein Thx 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
50S ribosomal protein L1 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
50S ribosomal protein L2 Chain: BD
Molecule details ›
Chain: BD
Length: 178 amino acids
Theoretical weight: 19.28 KDa
Source organisms: UniProt:
  • Canonical: P20276 (Residues: 163-203; Coverage: 17%)
  • Canonical: P04257 (Residues: 61-197; Coverage: 50%)
Gene names: rpl2, rplB, rrnAC1608
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: P02391 (Residues: 2-178; Coverage: 99%)
Gene name: rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L7/L12 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:
50S ribosomal protein L9 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:
50S ribosomal protein L11 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:
50S ribosomal protein L13 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
50S ribosomal protein L14 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
50S ribosomal protein L15 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
Ribosomal_L16 domain-containing protein 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
50S ribosomal protein L18 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
50S ribosomal protein L24e 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
50S ribosomal protein L22 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
50S ribosomal protein L23 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
50S ribosomal protein L24 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
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
50S ribosomal protein L29 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
50S ribosomal protein L30 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

214 review citations

Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy.
Meiser et al. (2020)
213 more

2 mentions without citation

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