› 8cdv

Electron Microscopy
4.73Å resolution

Rnase R bound to a 30S degradation intermediate (state II)

Released:
DOI: 10.2210/pdb8cdv/pdb
PDB entry 8cdv coloured by chain, front view.
PDB entry 8cdv coloured by chain, side view.
PDB entry 8cdv coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Structural basis of ribosomal 30S subunit degradation by RNase R.
Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H
OpenAccess logo Nature (2024)
PMID: 38326618
Related structures: EMD-16596

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-237943 (preferred)
Entry contents:
17 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (19 distinct):
Ribonuclease R Chain: C
Molecule details ›
Chain: C
Length: 779 amino acids
Theoretical weight: 88.89 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: O32231 (Residues: 1-779; Coverage: 100%)
Gene names: BSU33610, rnr, vacB, yvaJ
Sequence domains:
Small ribosomal subunit protein uS4 Chain: F
Molecule details ›
Chain: F
Length: 200 amino acids
Theoretical weight: 22.87 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21466 (Residues: 1-200; Coverage: 100%)
Gene names: BSU29660, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: G
Molecule details ›
Chain: G
Length: 166 amino acids
Theoretical weight: 17.65 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21467 (Residues: 1-166; Coverage: 100%)
Gene names: BSU01330, rpsE, spcA
Sequence domains:
Small ribosomal subunit protein uS7 Chain: H
Molecule details ›
Chain: H
Length: 156 amino acids
Theoretical weight: 17.92 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21469 (Residues: 1-156; Coverage: 100%)
Gene names: BSU01110, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: I
Molecule details ›
Chain: I
Length: 132 amino acids
Theoretical weight: 14.9 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12879 (Residues: 1-132; Coverage: 100%)
Gene names: BSU01300, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: J
Molecule details ›
Chain: J
Length: 130 amino acids
Theoretical weight: 14.34 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21470 (Residues: 1-130; Coverage: 100%)
Gene names: BSU01500, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: K
Molecule details ›
Chain: K
Length: 102 amino acids
Theoretical weight: 11.69 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21471 (Residues: 1-102; Coverage: 100%)
Gene names: BSU01150, rpsJ, tetA
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 138 amino acids
Theoretical weight: 15.25 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21472 (Residues: 1-138; Coverage: 100%)
Gene names: BSU01100, fun, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: M
Molecule details ›
Chain: M
Length: 121 amino acids
Theoretical weight: 13.82 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P20282 (Residues: 1-121; Coverage: 100%)
Gene names: BSU01410, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
Length: 89 amino acids
Theoretical weight: 10.6 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21473 (Residues: 1-89; Coverage: 100%)
Gene names: BSU16680, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 90 amino acids
Theoretical weight: 10.15 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21474 (Residues: 1-90; Coverage: 100%)
Gene names: BSU15990, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 87 amino acids
Theoretical weight: 10.22 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12874 (Residues: 1-87; Coverage: 100%)
Gene names: BSU01250, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein uS19 Chain: R
Molecule details ›
Chain: R
Length: 92 amino acids
Theoretical weight: 10.61 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21476 (Residues: 1-92; Coverage: 100%)
Gene names: BSU01200, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: S
Molecule details ›
Chain: S
Length: 88 amino acids
Theoretical weight: 9.62 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21477 (Residues: 1-88; Coverage: 100%)
Gene names: BSU25550, rpsT, yqeO
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS6 Chain: T
Molecule details ›
Chain: T
Length: 95 amino acids
Theoretical weight: 11.14 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21468 (Residues: 1-95; Coverage: 100%)
Gene names: BSU40910, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein bS18 Chain: U
Molecule details ›
Chain: U
Length: 79 amino acids
Theoretical weight: 8.99 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P21475 (Residues: 1-79; Coverage: 100%)
Gene names: BSU40890, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS11 Chain: V
Molecule details ›
Chain: V
Length: 131 amino acids
Theoretical weight: 13.95 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P04969 (Residues: 1-131; Coverage: 100%)
Gene names: BSU01420, rpsK
Sequence domains: Ribosomal protein S11
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1554 nucleotides
Theoretical weight: 503.37 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
RNA Substrate Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.58 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.73Å
Relevant EMDB volumes: EMD-16596

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