PDBe 4v42

X-ray diffraction
5.5Å resolution

Crystal structure of the ribosome at 5.5 A resolution.

Released:

Function and Biology Details

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
30S RIBOSOMAL PROTEIN S17 Chain: AT
Molecule details ›
Chain: AT
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus
30S RIBOSOMAL PROTEIN S18 Chain: AU
Molecule details ›
Chain: AU
Length: 88 amino acids
Theoretical weight: 10.24 KDa
Source organism: Thermus thermophilus
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
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 organism: Thermus thermophilus
UniProt:
  • Canonical: P60405 (Residues: 62-210, 211-218, 219-234; Coverage: 62%)
Gene names: TTHA1689, 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: Q5SHN8 (Residues: 52-180, 181-196; Coverage: 69%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
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: Q5SHN9 (Residues: 7-25, 26-46, 47-48, 49-62, 63-94, 95-118; Coverage: 51%)
Gene names: TTHA1691, rplD
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: Q5SHQ0 (Residues: 32-159; Coverage: 64%)
Gene names: TTHA1680, rplE
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: P0DOY8 (Residues: 2-177; Coverage: 98%)
Gene names: TTHA1677, 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: Q8VVE2 (Residues: 3-54, 55-97, 98-98, 99-125; Coverage: 98%)
Gene names: TTHA0210, 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: Q5SLQ1 (Residues: 1-86, 87-148; Coverage: 100%)
Gene names: TTHA0242, 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: Q5SLP6 (Residues: 2-139; Coverage: 94%)
Gene names: TTHA0247, rplK
Sequence domains: Ribosomal protein L11, RNA binding domain
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: P60488 (Residues: 14-89, 90-108, 109-125; Coverage: 66%)
Gene names: TTHA1465, rplM
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: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, 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: Q5SHQ7 (Residues: 12-26, 27-53, 54-85, 86-92, 93-121, 122-143; Coverage: 85%)
Gene names: TTHA1673, rplO
50S RIBOSOMAL PROTEIN L16 Chain: BP
Molecule details ›
Chain: BP
Length: 138 amino acids
Theoretical weight: 15.31 KDa
Source organism: Thermus thermophilus
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: Q5SHQ4 (Residues: 9-41, 42-46, 47-65, 66-90, 91-111; Coverage: 91%)
Gene names: TTHA1676, rplR
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: Q5SHP0 (Residues: 4-22, 23-58, 59-83; Coverage: 82%)
Gene names: TTHA1690, rplW
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: Q5SHP9 (Residues: 4-54; Coverage: 46%)
Gene names: TTHA1681, rplX
Sequence domains: KOW motif
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: Q5SHZ1 (Residues: 3-20, 21-49, 50-88; Coverage: 41%)
Gene names: TTHA1589, rpl25, rplY, rptL5
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: Q5SHP6 (Residues: 9-36, 37-67; Coverage: 82%)
Gene names: TTHA1684, rpmC
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

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°