› 5br8

X-ray diffraction
3.4Å resolution

Ambient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin

Released:
DOI: 10.2210/pdb5br8/pdb
PDB entry 5br8 coloured by chain, front view.
PDB entry 5br8 coloured by chain, side view.
PDB entry 5br8 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Entry authors: Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster A, Young ID, Michels-Clark T, Aquila A, Mengning L, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215876 (preferred)
Entry contents:
20 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (21 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
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
Structure domains:
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
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:
Structure domains:
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
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:
Structure domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
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:
Structure domains:
Small ribosomal subunit protein bS6 Chain: F
Molecule details ›
Chain: F
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
Structure domains: Alpha-Beta Plaits
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
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
Structure domains: Ribosomal protein S7 domain
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
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
Structure domains:
Small ribosomal subunit protein uS9 Chain: I
Molecule details ›
Chain: I
Length: 128 amino acids
Theoretical weight: 14.41 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
Structure domains: Ribosomal Protein S5; domain 2
Small ribosomal subunit protein uS10 Chain: J
Molecule details ›
Chain: J
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
Structure domains: Ribosomal protein S10 domain
Small ribosomal subunit protein uS11 Chain: K
Molecule details ›
Chain: K
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
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 135 amino acids
Theoretical weight: 14.97 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-132; Coverage: 99%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein uS13 Chain: M
Molecule details ›
Chain: M
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
Structure domains:
Small ribosomal subunit protein uS14 Chain: N
Molecule details ›
Chain: N
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
Structure domains: 30s Ribosomal Protein S14; Chain N
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
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
Structure domains: S15/NS1, RNA-binding
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
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
Structure domains: S16 Ribosomal Protein; Chain: A;
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
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
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein bS18 Chain: R
Molecule details ›
Chain: R
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Structure domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S
Molecule details ›
Chain: S
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
Structure domains: 30s Ribosomal Protein S19; Chain A
Small ribosomal subunit protein bS20 Chain: T
Molecule details ›
Chain: T
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Structure domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: U
Molecule details ›
Chain: U
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
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1522 nucleotides
Theoretical weight: 494.17 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand PAR 6 x PAR
Ligand MG 287 x MG
Ligand ZN 2 x ZN
9 modified residues:
Ligand PSU 3 x PSU
Ligand G7M 1 x G7M
Ligand M2G 1 x M2G
Ligand 5MC 4 x 5MC
Ligand 2MG 1 x 2MG
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand 0TD 1 x 0TD

Experiments and Validation Details

Entry percentile scores
X-ray source: SLAC LCLS BEAMLINE CXI
Spacegroup: P41212
Unit cell:
a: 401.3Å b: 401.3Å c: 176.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.193 0.234

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