PDBe 4v4s

X-ray diffraction
6.76Å resolution

Crystal structure of the whole ribosomal complex.

Released:

Function and Biology Details

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: P23370 (Residues: 1-101; Coverage: 100%)
Gene names: rps6, 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: P24319 (Residues: 1-138; Coverage: 100%)
Gene names: rps8, 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: P80375 (Residues: 1-105; Coverage: 100%)
Gene names: rps10, 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
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: P24320 (Residues: 1-61; Coverage: 100%)
Gene names: rps14, 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: P80378 (Residues: 1-89; Coverage: 100%)
Gene names: rps15, 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: P24321 (Residues: 1-105; Coverage: 100%)
Gene names: rps17, 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: P80382 (Residues: 1-88; Coverage: 100%)
Gene names: rps18, 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: P80381 (Residues: 1-93; Coverage: 100%)
Gene names: rps19, 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: P62661 (Residues: 1-106; Coverage: 100%)
Gene names: TT_C1031, 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: P62612 (Residues: 1-27; Coverage: 100%)
Gene name: rpsU
Sequence domains: 30S ribosomal protein Thx
Peptide chain release factor RF2 Chain: AY
Molecule details ›
Chain: AY
Length: 365 amino acids
Theoretical weight: 41.48 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SM01 (Residues: 20-27, 28-378; Coverage: 95%)
Gene names: TTHA0142, prfB
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
50S ribosomal protein L3 Chain: BE
Molecule details ›
Chain: BE
Length: 338 amino acids
Theoretical weight: 37.41 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L4 Chain: BF
Molecule details ›
Chain: BF
Length: 246 amino acids
Theoretical weight: 26.44 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L5 Chain: BG
Molecule details ›
Chain: BG
Length: 176 amino acids
Theoretical weight: 19.42 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L6 Chain: BH
Molecule details ›
Chain: BH
Length: 177 amino acids
Theoretical weight: 19.2 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L9 Chain: BI
Molecule details ›
Chain: BI
Length: 149 amino acids
Theoretical weight: 16.34 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L13 Chain: BN
Molecule details ›
Chain: BN
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L14 Chain: BO
Molecule details ›
Chain: BO
Length: 122 amino acids
Theoretical weight: 13.37 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L15 Chain: BP
Molecule details ›
Chain: BP
Length: 164 amino acids
Theoretical weight: 17.87 KDa
Source organism: Thermus thermophilus
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
50S ribosomal protein L19 Chain: BT
Molecule details ›
Chain: BT
Length: 66 amino acids
Theoretical weight: 7.23 KDa
Source organism: Thermus thermophilus
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
50S ribosomal protein 24 Chain: BY
Molecule details ›
Chain: BY
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Thermus thermophilus
50S ribosomal protein CTC Chain: BZ
Molecule details ›
Chain: BZ
Length: 253 amino acids
Theoretical weight: 27 KDa
Source organism: Thermus thermophilus
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
50S ribosomal protein L21 Chain: BV
Molecule details ›
Chain: BV
Length: 100 amino acids
Theoretical weight: 11.17 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L29 Chain: B2
Molecule details ›
Chain: B2
Length: 70 amino acids
Theoretical weight: 7.76 KDa
Source organism: Thermus thermophilus
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
50S ribosomal protein L31 Chain: B4
Molecule details ›
Chain: B4
Length: 73 amino acids
Theoretical weight: 8.6 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L32 Chain: B5
Molecule details ›
Chain: B5
Length: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L33 Chain: B6
Molecule details ›
Chain: B6
Length: 82 amino acids
Theoretical weight: 9.29 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L34 Chain: B7
Molecule details ›
Chain: B7
Length: 47 amino acids
Theoretical weight: 5.63 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L35 Chain: B8
Molecule details ›
Chain: B8
Length: 64 amino acids
Theoretical weight: 7.26 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L36 Chain: B9
Molecule details ›
Chain: B9
Length: 36 amino acids
Theoretical weight: 4.27 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L11 Chain: BK
Molecule details ›
Chain: BK
Length: 141 amino acids
Theoretical weight: 15.11 KDa
Source organism: Thermus thermophilus
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*AP*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:

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P43212
Unit cell:
a: 520.213Å b: 520.213Å c: 365.898Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.344 0.341 0.356
Expression system: Escherichia coli