› 5o5j

Electron Microscopy
3.45Å resolution

Structure of the 30S small ribosomal subunit from Mycobacterium smegmatis

Released:
DOI: 10.2210/pdb5o5j/pdb
PDB entry 5o5j coloured by chain, front view.
PDB entry 5o5j coloured by chain, side view.
PDB entry 5o5j coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Hentschel J, Burnside C, Mignot I, Leibundgut M, Boehringer D, Ban N
Cell Rep 20 149-160 (2017)
PMID: 28683309
Related structures: EMD-3748

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
PDBe Complex ID:
PDB-CPX-499238 (preferred)
Entry contents:
21 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (24 distinct):
Ribosomal protein mS38 C-terminal domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 33 amino acids
Theoretical weight: 4.16 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QR10 (Residues: 1-33; Coverage: 100%)
Gene name: MSMEG_0945
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 30.19 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD7 (Residues: 1-275; Coverage: 100%)
Gene names: MSMEG_1442, MSMEI_1406, rpsC
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 201 amino acids
Theoretical weight: 23.42 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL7 (Residues: 1-201; Coverage: 100%)
Gene names: MSMEG_1523, MSMEI_1487, rpsD
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 214 amino acids
Theoretical weight: 21.95 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG6 (Residues: 1-214; Coverage: 100%)
Gene names: MSMEG_1472, MSMEI_1436, rpsE
Sequence domains:
30S ribosomal protein S6 Chain: F
Molecule details ›
Chain: F
Length: 96 amino acids
Theoretical weight: 10.99 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
Length: 156 amino acids
Theoretical weight: 17.66 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS97 (Residues: 1-156; Coverage: 100%)
Gene names: MSMEG_1399, MSMEI_1361, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 132 amino acids
Theoretical weight: 14.49 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG3 (Residues: 1-132; Coverage: 100%)
Gene names: MSMEG_1469, MSMEI_1433, rpsH
Sequence domains: Ribosomal protein S8
Structure domains:
Small ribosomal subunit protein uS9 Chain: I
Molecule details ›
Chain: I
Length: 150 amino acids
Theoretical weight: 16.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSP9 (Residues: 1-150; Coverage: 100%)
Gene names: MSMEG_1557, MSMEI_1520, 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: 101 amino acids
Theoretical weight: 11.45 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD0 (Residues: 1-101; Coverage: 100%)
Gene names: MSMEG_1435, MSMEI_1399, 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: 138 amino acids
Theoretical weight: 14.67 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL6 (Residues: 1-138; Coverage: 100%)
Gene names: MSMEG_1522, MSMEI_1486, rpsK
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 124 amino acids
Theoretical weight: 13.9 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS96 (Residues: 1-124; Coverage: 100%)
Gene names: MSMEG_1398, MSMEI_1360, 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: 124 amino acids
Theoretical weight: 14.25 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL5 (Residues: 1-124; Coverage: 100%)
Gene names: MSMEG_1521, MSMEI_1485, rpsM
Sequence domains: Ribosomal protein S13/S18
Structure domains:
Small ribosomal subunit protein uS14B Chain: N
Molecule details ›
Chain: N
Length: 61 amino acids
Theoretical weight: 6.98 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG2 (Residues: 1-61; Coverage: 100%)
Gene names: MSMEG_1468, MSMEI_1432, 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: 10.37 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVQ3 (Residues: 1-89; Coverage: 100%)
Gene names: MSMEG_2654, MSMEI_2591, rpsO
Sequence domains: Ribosomal protein S15
Structure domains: S15/NS1, RNA-binding
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 156 amino acids
Theoretical weight: 16.8 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QV37 (Residues: 1-156; Coverage: 100%)
Gene names: MSMEG_2435, MSMEI_2374, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 98 amino acids
Theoretical weight: 11.13 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSE0 (Residues: 1-98; Coverage: 100%)
Gene names: MSMEG_1445, MSMEI_1409, rpsQ
Sequence domains: Ribosomal protein S17
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein bS18B Chain: R
Molecule details ›
Chain: R
Length: 84 amino acids
Theoretical weight: 9.52 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7F7 (Residues: 1-84; Coverage: 100%)
Gene names: MSMEG_6895, MSMEI_6711, rpsR1, rpsR2
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: 10.8 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD5 (Residues: 1-93; Coverage: 100%)
Gene names: MSMEG_1440, MSMEI_1404, 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: 86 amino acids
Theoretical weight: 9.56 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R102 (Residues: 1-86; Coverage: 100%)
Gene names: MSMEG_4571, MSMEI_4459, rpsT
Sequence domains: Ribosomal protein S20
Structure domains: Ribosomal protein S20
Small ribosomal subunit protein uS2 Chain: V
Molecule details ›
Chain: V
Length: 277 amino acids
Theoretical weight: 30.15 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVB8 (Residues: 1-277; Coverage: 100%)
Gene names: MSMEG_2519, MSMEI_2460, rpsB
Sequence domains: Ribosomal protein S2
Structure domains:
Large ribosomal subunit protein bL31 Chain: g
Molecule details ›
Chain: g
Length: 75 amino acids
Theoretical weight: 8.31 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R215 (Residues: 1-75; Coverage: 100%)
Gene names: MSMEG_4951, MSMEI_4823, rpmE
Sequence domains: Ribosomal protein L31
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1528 nucleotides
Theoretical weight: 495.37 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
tRNA-Phe anticodon stem Chain: W
Molecule details ›
Chain: W
Length: 19 nucleotides
Theoretical weight: 6.14 KDa
Messenger RNA Chain: X
Molecule details ›
Chain: X
Length: 6 nucleotides
Theoretical weight: 1.79 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 217 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.451Å
Relevant EMDB volumes: EMD-3748

Quick links

Citations

4 review citations

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.
Poitevin et al. (2020)
3 more

4 mentions without citation

Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM.
Bendre et al. (2021)
3 more