› 5no2

Electron Microscopy
5.16Å resolution

RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate)

Released:
DOI: 10.2210/pdb5no2/pdb
PDB entry 5no2 coloured by chain, front view.
PDB entry 5no2 coloured by chain, side view.
PDB entry 5no2 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket.
López-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR
Nucleic Acids Res 45 6945-6959 (2017)
PMID: 28482099
Related structures: EMD-3661

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215813 (preferred)
Entry contents:
18 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (19 distinct):
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 155 amino acids
Theoretical weight: 16.36 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W1 (Residues: 10-164; Coverage: 93%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: F
Molecule details ›
Chain: F
Length: 106 amino acids
Theoretical weight: 12.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02358 (Residues: 1-106; Coverage: 79%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
Length: 130 amino acids
Theoretical weight: 14.54 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02359 (Residues: 2-131; Coverage: 73%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: 99%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: I
Molecule details ›
Chain: I
Length: 127 amino acids
Theoretical weight: 14.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7X3 (Residues: 4-130; Coverage: 98%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: J
Molecule details ›
Chain: J
Length: 99 amino acids
Theoretical weight: 11.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R5 (Residues: 4-102; Coverage: 96%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 12.49 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 13-129; Coverage: 91%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 14 amino acids
Theoretical weight: 1.64 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S3 (Residues: 2-15; Coverage: 11%)
Gene names: JW3304, b3342, rpsL, strA
Small ribosomal subunit protein uS13 Chain: M
Molecule details ›
Chain: M
Length: 114 amino acids
Theoretical weight: 12.63 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S9 (Residues: 2-115; Coverage: 97%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: N
Molecule details ›
Chain: N
Length: 100 amino acids
Theoretical weight: 11.48 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG59 (Residues: 2-101; Coverage: 99%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: 99%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG63 (Residues: 4-83; Coverage: 95%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: R
Molecule details ›
Chain: R
Length: 55 amino acids
Theoretical weight: 6.47 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T7 (Residues: 20-74; Coverage: 73%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S
Molecule details ›
Chain: S
Length: 79 amino acids
Theoretical weight: 9.06 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U3 (Residues: 3-81; Coverage: 86%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: T
Molecule details ›
Chain: T
Length: 86 amino acids
Theoretical weight: 9.58 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U7 (Residues: 2-87; Coverage: 99%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit biogenesis GTPase RsgA Chain: Z
Molecule details ›
Chain: Z
Length: 313 amino acids
Theoretical weight: 34.85 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P39286 (Residues: 34-346; Coverage: 89%)
Gene names: JW4122, b4161, engC, rsgA, yjeQ
Sequence domains: RsgA GTPase
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1534 nucleotides
Theoretical weight: 497.4 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 71 x MG
Ligand ZN 1 x ZN
Ligand GNP 1 x GNP
7 modified residues:
Ligand PSU 1 x PSU
Ligand G7M 1 x G7M
Ligand 2MG 3 x 2MG
Ligand 5MC 2 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 5.16Å
Relevant EMDB volumes: EMD-3661
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

RNA-binding proteins in bacteria.
Holmqvist et al. (2018)
2 more

4 mentions without citation

Measurement of atom resolvability in cryo-EM maps with Q-scores.
Pintilie et al. (2020)
3 more