Structure analysis

Structure of the SmrB-bound E. coli disome - stalled 70S ribosome

Electron Microscopy
3.37Å resolution
Assembly composition:
hetero 58-mer (preferred)
Entry contents: 53 distinct polypeptide molecules
5 distinct RNA molecules

Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 58-mer
Accessible surface area: 793236.15 Å2
Buried surface area: 258085.13 Å2
Dissociation area: 714.45 Å2
Dissociation energy (ΔGdiss): -0.21 kcal/mol
Dissociation entropy (TΔSdiss): 13.71 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279459

Macromolecules

Chain: B
Length: 183 amino acids
Theoretical weight: 20.94 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8B2 (Residues: 1-183; Coverage: 100%)
Gene names: JW2328, b2331, smrB, yfcN
Pfam: Smr domain
InterPro:

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Chain: s
Length: 179 amino acids
Theoretical weight: 20.53 KDa
Source organism: Vibrio alginolyticus
Expression system: Escherichia coli

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Chain: R
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Pfam: Ribosomal protein L4/L1 family
InterPro:

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Chain: W
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Pfam: Ribosomal protein L13
InterPro:

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Chain: X
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Pfam: Ribosomal protein L14p/L23e
InterPro:

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Chain: a
Length: 127 amino acids
Theoretical weight: 14.34 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Pfam: Ribosomal protein L17
InterPro:

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Chain: b
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Pfam: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
InterPro:

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Chain: c
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Pfam: Ribosomal protein L19
InterPro:

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Chain: d
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Pfam: Ribosomal protein L20
InterPro:

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Chain: e
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Pfam: Ribosomal prokaryotic L21 protein
InterPro:

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Chain: j
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Pfam: Ribosomal L27 protein
InterPro:

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Chain: l
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Pfam: Ribosomal L29 protein
InterPro:

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Chain: n
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Pfam: Ribosomal L32p protein family
InterPro:

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Chain: p
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Pfam: Ribosomal protein L34
InterPro:

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Chain: r
Length: 55 amino acids
Theoretical weight: 6.32 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Pfam: Ribosomal protein L36
InterPro:

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Chain: 7
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W7 (Residues: 1-130; Coverage: 100%)
Gene names: JW3268, b3306, rpsH
Pfam: Ribosomal protein S8
InterPro:

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Chain: 9
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R5 (Residues: 1-103; Coverage: 100%)
Gene names: JW3283, b3321, nusE, rpsJ
Pfam: Ribosomal protein S10p/S20e
InterPro:

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Chain: D
Length: 129 amino acids
Theoretical weight: 13.84 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R9 (Residues: 1-129; Coverage: 100%)
Gene names: JW3259, b3297, rpsK
Pfam: Ribosomal protein S11
InterPro:

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Chain: E
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S3 (Residues: 1-124; Coverage: 100%)
Gene names: JW3304, b3342, rpsL, strA
Pfam: Ribosomal protein S12/S23
InterPro:

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Chain: G
Length: 101 amino acids
Theoretical weight: 11.56 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG59 (Residues: 1-101; Coverage: 100%)
Gene names: JW3269, b3307, rpsN
Pfam: Ribosomal protein S14p/S29e
InterPro:

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Chain: H
Length: 89 amino acids
Theoretical weight: 10.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ4 (Residues: 1-89; Coverage: 100%)
Gene names: JW3134, b3165, rpsO, secC
Pfam: Ribosomal protein S15
InterPro:

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Chain: I
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli UMEA 3162-1
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Pfam: Ribosomal protein S16
InterPro:

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Chain: J
Length: 84 amino acids
Theoretical weight: 9.69 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG63 (Residues: 1-84; Coverage: 100%)
Gene names: JW3273, b3311, neaA, rpsQ
Pfam: Ribosomal protein S17
InterPro:

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Chain: t
Length: 92 amino acids
Theoretical weight: 10.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U3 (Residues: 1-92; Coverage: 100%)
Gene names: JW3278, b3316, rpsS
Pfam: Ribosomal protein S19
InterPro:

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Chain: u
Length: 87 amino acids
Theoretical weight: 9.69 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 1-87; Coverage: 100%)
Gene names: JW0022, b0023, rpsT
Pfam: Ribosomal protein S20
InterPro:

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Name: A-site tRNA
Representative chains: A
Length: 73 nucleotides
Theoretical weight: 23.55 KDa
Rfam: tRNA

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Name: P-site tRNA
Representative chains: M
Length: 75 nucleotides
Theoretical weight: 24.06 KDa
Rfam: tRNA

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Name: 5S ribosomal RNA
Representative chains: O
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Rfam: 5S ribosomal RNA

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Name: 23S ribosomal RNA
Representative chains: N
Length: 2903 nucleotides
Theoretical weight: 941.31 KDa
Rfam: Bacterial large subunit ribosomal RNA

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Name: 16S ribosomal RNA
Representative chains: 0
Length: 1539 nucleotides
Theoretical weight: 498.73 KDa
Rfam: Bacterial small subunit ribosomal RNA

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