› 3j3v

Electron Microscopy
13.3Å resolution

Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)

Released:
DOI: 10.2210/pdb3j3v/pdb
PDB entry 3j3v coloured by chain, front view.
PDB entry 3j3v coloured by chain, side view.
PDB entry 3j3v coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit.
Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N
Nucleic Acids Res 41 7073-83 (2013)
PMID: 23700310
Related structures: EMD-5642

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128360 (preferred)
Entry contents:
22 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (24 distinct):
Large ribosomal subunit protein bL32 Chain: 0
Molecule details ›
Chain: 0
Length: 59 amino acids
Theoretical weight: 6.75 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: O34687 (Residues: 1-59; Coverage: 100%)
Gene names: BSU15080, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
Chain: 2
Length: 44 amino acids
Theoretical weight: 5.27 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P05647 (Residues: 1-44; Coverage: 100%)
Gene names: BSU41060, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein uL1 Chain: 5
Molecule details ›
Chain: 5
Length: 232 amino acids
Theoretical weight: 25.03 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: Q06797 (Residues: 1-232; Coverage: 100%)
Gene names: BSU01030, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL11 Chain: 6
Molecule details ›
Chain: 6
Length: 141 amino acids
Theoretical weight: 14.95 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: Q06796 (Residues: 1-141; Coverage: 100%)
Gene names: BSU01020, relC, rplK, tsp6
Sequence domains:
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 277 amino acids
Theoretical weight: 30.34 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42919 (Residues: 1-277; Coverage: 100%)
Gene names: BSU01190, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.72 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42920 (Residues: 1-209; Coverage: 100%)
Gene names: BSU01160, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 207 amino acids
Theoretical weight: 22.42 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42921 (Residues: 1-207; Coverage: 100%)
Gene names: BSU01170, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.18 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12877 (Residues: 1-179; Coverage: 100%)
Gene names: BSU01280, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 179 amino acids
Theoretical weight: 19.54 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P46898 (Residues: 1-179; Coverage: 100%)
Gene names: BSU01310, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: J
Molecule details ›
Chain: J
Length: 145 amino acids
Theoretical weight: 16.41 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P70974 (Residues: 1-145; Coverage: 100%)
Gene names: BSU01490, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: K
Molecule details ›
Chain: K
Length: 122 amino acids
Theoretical weight: 13.18 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12875 (Residues: 1-122; Coverage: 100%)
Gene names: BSU01260, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: L
Molecule details ›
Chain: L
Length: 146 amino acids
Theoretical weight: 15.41 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P19946 (Residues: 1-146; Coverage: 100%)
Gene names: BSU01350, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein bL17 Chain: N
Molecule details ›
Chain: N
Length: 120 amino acids
Theoretical weight: 13.77 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P20277 (Residues: 1-120; Coverage: 100%)
Gene names: BSU01440, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: O
Molecule details ›
Chain: O
Length: 120 amino acids
Theoretical weight: 12.99 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P46899 (Residues: 1-120; Coverage: 100%)
Gene names: BSU01320, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: P
Molecule details ›
Chain: P
Length: 115 amino acids
Theoretical weight: 13.42 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: O31742 (Residues: 1-115; Coverage: 100%)
Gene names: BSU16040, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: Q
Molecule details ›
Chain: Q
Length: 119 amino acids
Theoretical weight: 13.67 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P55873 (Residues: 1-119; Coverage: 100%)
Gene names: BSU28850, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: R
Molecule details ›
Chain: R
Length: 102 amino acids
Theoretical weight: 11.3 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P26908 (Residues: 1-102; Coverage: 100%)
Gene names: BSU27960, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: S
Molecule details ›
Chain: S
Length: 113 amino acids
Theoretical weight: 12.48 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42060 (Residues: 1-113; Coverage: 100%)
Gene names: BSU01210, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: T
Molecule details ›
Chain: T
Length: 95 amino acids
Theoretical weight: 10.98 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42924 (Residues: 1-95; Coverage: 100%)
Gene names: BSU01180, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: U
Molecule details ›
Chain: U
Length: 103 amino acids
Theoretical weight: 11.17 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P0CI78 (Residues: 1-103; Coverage: 100%)
Gene names: BSU01270, rplX
Sequence domains:
Large ribosomal subunit protein uL29 Chain: X
Molecule details ›
Chain: X
Length: 66 amino acids
Theoretical weight: 7.73 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12873 (Residues: 1-66; Coverage: 100%)
Gene names: BSU01240, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: Y
Molecule details ›
Chain: Y
Length: 59 amino acids
Theoretical weight: 6.65 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P19947 (Residues: 1-59; Coverage: 100%)
Gene names: BSU01340, rpmD
Sequence domains: Ribosomal protein L30p/L7e
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2927 nucleotides
Theoretical weight: 949.32 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 119 nucleotides
Theoretical weight: 38.42 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 13.3Å
Relevant EMDB volumes: EMD-5642

Quick links

Citations

8 review citations

Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo.
de la Cruz et al. (2015)
7 more

3 mentions without citation

Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit.
Li et al. (2013)
2 more