› 8wif

Electron Microscopy
2.9Å resolution

Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome and RafH.

Released:
DOI: 10.2210/pdb8wif/pdb
PDB entry 8wif coloured by chain, front view.
PDB entry 8wif coloured by chain, side view.
PDB entry 8wif coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.
Kumar N, Sharma S, Kaushal PS
OpenAccess logo Nat Commun 15 638 (2024)
PMID: 38245551
Related structures: EMD-37565

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-499242 (preferred)
Entry contents:
22 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (23 distinct):
Ribosomal protein mS38 C-terminal domain-containing protein Chain: v
Molecule details ›
Chain: v
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: d
Molecule details ›
Chain: d
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:
Small ribosomal subunit protein uS4 Chain: e
Molecule details ›
Chain: e
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:
Small ribosomal subunit protein uS5 Chain: f
Molecule details ›
Chain: f
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:
Small ribosomal subunit protein bS6 Chain: g
Molecule details ›
Chain: g
Length: 96 amino acids
Theoretical weight: 10.99 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7F9 (Residues: 1-90; Coverage: 100%)
Gene names: MSMEG_6897, MSMEI_6713, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: h
Molecule details ›
Chain: h
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: i
Molecule details ›
Chain: i
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
Small ribosomal subunit protein uS9 Chain: j
Molecule details ›
Chain: j
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
Small ribosomal subunit protein uS10 Chain: k
Molecule details ›
Chain: k
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
Small ribosomal subunit protein uS11 Chain: l
Molecule details ›
Chain: l
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
Small ribosomal subunit protein uS12 Chain: m
Molecule details ›
Chain: m
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
Small ribosomal subunit protein uS13 Chain: n
Molecule details ›
Chain: n
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
Small ribosomal subunit protein uS14A Chain: o
Molecule details ›
Chain: o
Length: 101 amino acids
Theoretical weight: 11.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R550 (Residues: 1-101; Coverage: 100%)
Gene names: MSMEG_6066, MSMEI_5906, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: p
Molecule details ›
Chain: p
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
Small ribosomal subunit protein bS16 Chain: q
Molecule details ›
Chain: q
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: r
Molecule details ›
Chain: r
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
Small ribosomal subunit protein bS18B Chain: s
Molecule details ›
Chain: s
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
Small ribosomal subunit protein uS19 Chain: t
Molecule details ›
Chain: t
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
Small ribosomal subunit protein bS20 Chain: u
Molecule details ›
Chain: u
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
Small ribosomal subunit protein uS2 Chain: c
Molecule details ›
Chain: c
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
Large ribosomal subunit protein bL31 Chain: x
Molecule details ›
Chain: x
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
Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein Chain: w
Molecule details ›
Chain: w
Length: 264 amino acids
Theoretical weight: 29.9 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0QZ86 (Residues: 1-258; Coverage: 100%)
Gene name: MSMEG_3935
Sequence domains:
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1528 nucleotides
Theoretical weight: 495.37 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-37565
Expression system: Escherichia coli BL21(DE3)

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