› 9gut

Electron Microscopy
2.8Å resolution

30S mRNA delivery complex (bS1 resolved)

Released:
DOI: 10.2210/pdb9gut/pdb
PDB entry 9gut coloured by chain, front view.
PDB entry 9gut coloured by chain, side view.
PDB entry 9gut coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Molecular basis of mRNA delivery to the bacterial ribosome.
Webster MW, Chauvier A, Rahil H, Graziadei A, Charles K, Miropolskaya N, Takacs M, Saint-André C, Rappsilber J, Walter NG, Weixlbaumer A
Science 386 eado8476 (2024)
PMID: 39607923
Related structures: EMD-51619

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-284888 (preferred)
Entry contents:
21 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (24 distinct):
Small ribosomal subunit protein bS1 Chain: B
Molecule details ›
Chain: B
Length: 557 amino acids
Theoretical weight: 61.24 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0AG67 (Residues: 1-557; Coverage: 100%)
Gene names: JW0894, b0911, rpsA, ssyF
Sequence domains: S1 RNA binding domain
Small ribosomal subunit protein uS2 Chain: C
Molecule details ›
Chain: C
Length: 241 amino acids
Theoretical weight: 26.78 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V0 (Residues: 1-241; Coverage: 100%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: D
Molecule details ›
Chain: D
Length: 233 amino acids
Theoretical weight: 26.03 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V3 (Residues: 1-233; Coverage: 100%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: E
Molecule details ›
Chain: E
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V8 (Residues: 1-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: F
Molecule details ›
Chain: F
Length: 156 amino acids
Theoretical weight: 16.48 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W1 (Residues: 10-165; Coverage: 93%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6 Chain: G
Molecule details ›
Chain: G
Length: 131 amino acids
Theoretical weight: 15.2 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P02358 (Residues: 1-131; Coverage: 97%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: H
Molecule details ›
Chain: H
Length: 156 amino acids
Theoretical weight: 17.64 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P02359 (Residues: 1-156; Coverage: 87%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: I
Molecule details ›
Chain: I
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W7 (Residues: 1-130; Coverage: 100%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: J
Molecule details ›
Chain: J
Length: 130 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7X3 (Residues: 1-130; Coverage: 100%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: K
Molecule details ›
Chain: K
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R5 (Residues: 1-103; Coverage: 100%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: L
Molecule details ›
Chain: L
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 1-129; Coverage: 100%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: M
Molecule details ›
Chain: M
Length: 124 amino acids
Theoretical weight: 13.81 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S3 (Residues: 1-124; Coverage: 100%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: N
Molecule details ›
Chain: N
Length: 118 amino acids
Theoretical weight: 13.13 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S9 (Residues: 1-118; Coverage: 100%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: O
Molecule details ›
Chain: O
Length: 101 amino acids
Theoretical weight: 11.61 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0AG59 (Residues: 1-101; Coverage: 100%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: P
Molecule details ›
Chain: P
Length: 89 amino acids
Theoretical weight: 10.29 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ4 (Residues: 1-89; Coverage: 100%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: Q
Molecule details ›
Chain: Q
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli K-12
Expression system: 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: R
Molecule details ›
Chain: R
Length: 84 amino acids
Theoretical weight: 9.72 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0AG63 (Residues: 1-84; Coverage: 100%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: S
Molecule details ›
Chain: S
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T7 (Residues: 1-75; Coverage: 100%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: T
Molecule details ›
Chain: T
Length: 92 amino acids
Theoretical weight: 10.46 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U3 (Residues: 1-92; Coverage: 100%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: U
Molecule details ›
Chain: U
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U7 (Residues: 1-87; Coverage: 100%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: V
Molecule details ›
Chain: V
Length: 71 amino acids
Theoretical weight: 8.52 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P68679 (Residues: 1-71; Coverage: 100%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3082 nucleotides
Theoretical weight: 999.08 KDa
Sequence domains:
  • Bacterial small subunit ribosomal RNA
  • Archaeal small subunit ribosomal RNA
    • tRNA(fmet) P-site Chain: W
    Molecule details ›
    Chain: W
    Length: 77 nucleotides
    Theoretical weight: 24.83 KDa
    Sequence domains: tRNA
    Messenger RNA Chain: X
    Molecule details ›
    Chain: X
    Length: 53 nucleotides
    Theoretical weight: 17.06 KDa

    Ligands and Environments

    1 bound ligand:
    Ligand MG 137 x MG
    12 modified residues:
    Ligand PSU 3 x PSU
    Ligand G7M 2 x G7M
    Ligand 2MG 6 x 2MG
    Ligand 5MC 4 x 5MC
    Ligand 4OC 2 x 4OC
    Ligand UR3 2 x UR3
    Ligand MA6 4 x MA6
    Ligand D2T 1 x D2T
    Ligand 4SU 1 x 4SU
    Ligand H2U 1 x H2U
    Ligand OMC 1 x OMC
    Ligand 5MU 1 x 5MU

    Experiments and Validation Details

    Entry percentile scores
    Resolution: 2.8Å
    Relevant EMDB volumes: EMD-51619
    Expression system: Escherichia coli K-12

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