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E. coli 50S ribosome bound to compound streptogramin analogs SA1 and SB1

Electron Microscopy
2.35Å resolution
PDB entry 8e32 coloured by chain, front view.
PDB entry 8e32 coloured by chain, side view.
PDB entry 8e32 coloured by chain, top view.
Source organism: Escherichia coli
Assembly composition:
hetero decamer (preferred)
Entry contents: 8 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Large ribosomal protein and RNA
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Multimeric state: hetero decamer
Accessible surface area: 459980.55 Å2
Buried surface area: 73711.75 Å2
Dissociation area: 705.56 Å2
Dissociation energy (ΔGdiss): 0.48 kcal/mol
Dissociation entropy (TΔSdiss): 15.6 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-232403

Macromolecules

Large ribosomal subunit protein uL2
Chain: K
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 2-272; Coverage: 99%)
Gene names: JW3279, b3317, rplB
Pfam:
Large ribosomal subunit protein uL2 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein uL2 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein uL2 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein uL15
Chain: L
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Pfam: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL15 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein uL15 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein uL15 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein uL4
Chain: M
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Pfam: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL4 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein uL4 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein uL4 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein uL3
Chain: N
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Pfam: Ribosomal protein L3
Large ribosomal subunit protein uL3 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein uL3 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein uL3 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein uL13
Chain: O
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Pfam: Ribosomal protein L13
Large ribosomal subunit protein uL13 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein uL13 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein uL13 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein uL22
Chain: P
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Pfam: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL22 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein uL22 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein uL22 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein bL32
Chain: Q
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 2-57; Coverage: 98%)
Gene names: JW1075, b1089, rpmF
Pfam: Ribosomal L32p protein family
Large ribosomal subunit protein bL32 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein bL32 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein bL32 in PDB entry 8e32, assembly 1, top view.
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Large ribosomal subunit protein bL34
Chain: R
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Pfam: Ribosomal protein L34
Large ribosomal subunit protein bL34 in PDB entry 8e32, assembly 1, front view.
Large ribosomal subunit protein bL34 in PDB entry 8e32, assembly 1, side view.
Large ribosomal subunit protein bL34 in PDB entry 8e32, assembly 1, top view.
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RNA chain I
Name: 23S ribosomal RNA
Representative chains: I
Length: 2904 nucleotides
Theoretical weight: 941.8 KDa
Rfam: Bacterial large subunit ribosomal RNA
23S ribosomal RNA in PDB entry 8e32, assembly 1, front view.
23S ribosomal RNA in PDB entry 8e32, assembly 1, side view.
23S ribosomal RNA in PDB entry 8e32, assembly 1, top view.
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RNA chain J
Name: 5S ribosomal RNA
Representative chains: J
Length: 118 nucleotides
Theoretical weight: 38.18 KDa
Rfam: 5S ribosomal RNA
5S ribosomal RNA in PDB entry 8e32, assembly 1, front view.
5S ribosomal RNA in PDB entry 8e32, assembly 1, side view.
5S ribosomal RNA in PDB entry 8e32, assembly 1, top view.
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