8uu5

Electron Microscopy
3Å resolution

Cryo-EM structure of the Listeria innocua 70S ribosome (head-swiveled) in complex with pe/E-tRNA (structure I-B)

Released:
Primary publication:
Mechanistic insights into the alternative ribosome recycling by HflXr.
OpenAccess logo Nucleic Acids Res (2024)
PMID: 38407413
Related structures: EMD-42557

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 51-mer (preferred)
PDBe Complex ID:
PDB-CPX-268752 (preferred)
Entry contents:
46 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (51 distinct):
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 249 amino acids
Theoretical weight: 28.36 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 218 amino acids
Theoretical weight: 24.59 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 200 amino acids
Theoretical weight: 22.72 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 167 amino acids
Theoretical weight: 17.52 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 97 amino acids
Theoretical weight: 11.51 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 17.85 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 132 amino acids
Theoretical weight: 14.67 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 130 amino acids
Theoretical weight: 14.47 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 102 amino acids
Theoretical weight: 11.7 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.81 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 137 amino acids
Theoretical weight: 15.22 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 121 amino acids
Theoretical weight: 13.74 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS14 Chain: n
Molecule details ›
Chain: n
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.66 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 90 amino acids
Theoretical weight: 10.4 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 87 amino acids
Theoretical weight: 10.06 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 79 amino acids
Theoretical weight: 9.12 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 92 amino acids
Theoretical weight: 10.5 KDa
Source organism: Listeria innocua
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 84 amino acids
Theoretical weight: 9.19 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 277 amino acids
Theoretical weight: 30.57 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.88 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 207 amino acids
Theoretical weight: 22.64 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.02 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 178 amino acids
Theoretical weight: 19.43 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL13 Chain: L
Molecule details ›
Chain: L
Length: 145 amino acids
Theoretical weight: 16.23 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL14 Chain: M
Molecule details ›
Chain: M
Length: 122 amino acids
Theoretical weight: 13.25 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL15 Chain: N
Molecule details ›
Chain: N
Length: 146 amino acids
Theoretical weight: 15.83 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL16 Chain: O
Molecule details ›
Chain: O
Length: 144 amino acids
Theoretical weight: 16.17 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL17 Chain: P
Molecule details ›
Chain: P
Length: 135 amino acids
Theoretical weight: 15.24 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL18 Chain: Q
Molecule details ›
Chain: Q
Length: 119 amino acids
Theoretical weight: 13.11 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL19 Chain: R
Molecule details ›
Chain: R
Length: 114 amino acids
Theoretical weight: 13.09 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL20 Chain: S
Molecule details ›
Chain: S
Length: 119 amino acids
Theoretical weight: 13.72 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL21 Chain: T
Molecule details ›
Chain: T
Length: 102 amino acids
Theoretical weight: 11.22 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL22 Chain: U
Molecule details ›
Chain: U
Length: 118 amino acids
Theoretical weight: 12.9 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL23 Chain: V
Molecule details ›
Chain: V
Length: 94 amino acids
Theoretical weight: 10.95 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL24 Chain: W
Molecule details ›
Chain: W
Length: 103 amino acids
Theoretical weight: 11.22 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL27 Chain: Y
Molecule details ›
Chain: Y
Length: 96 amino acids
Theoretical weight: 10.57 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL28 Chain: Z
Molecule details ›
Chain: Z
Length: 62 amino acids
Theoretical weight: 7.01 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL29 Chain: 1
Molecule details ›
Chain: 1
Length: 63 amino acids
Theoretical weight: 7.41 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein uL30 Chain: 2
Molecule details ›
Chain: 2
Length: 59 amino acids
Theoretical weight: 6.5 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL31B Chain: 3
Molecule details ›
Chain: 3
Length: 81 amino acids
Theoretical weight: 9.27 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL32 Chain: 4
Molecule details ›
Chain: 4
Length: 57 amino acids
Theoretical weight: 6.53 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL33 Chain: 5
Molecule details ›
Chain: 5
Length: 49 amino acids
Theoretical weight: 6.02 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL34 Chain: 6
Molecule details ›
Chain: 6
Length: 44 amino acids
Theoretical weight: 5.32 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL35 Chain: 7
Molecule details ›
Chain: 7
Length: 66 amino acids
Theoretical weight: 7.75 KDa
Source organism: Listeria innocua
Large ribosomal subunit protein bL36 Chain: 8
Molecule details ›
Chain: 8
Length: 37 amino acids
Theoretical weight: 4.34 KDa
Source organism: Listeria innocua
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1550 nucleotides
Theoretical weight: 501.95 KDa
Source organism: Listeria innocua
Sequence domains: Bacterial small subunit ribosomal RNA
pe/E Hybrid State Phenylalanine tRNA Chain: x
Molecule details ›
Chain: x
Length: 76 nucleotides
Theoretical weight: 24.64 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli HB101
Sequence domains: tRNA
F-Stop mRNA Chain: w
Molecule details ›
Chain: w
Length: 21 nucleotides
Theoretical weight: 6.79 KDa
Source organism: Escherichia phage T4
Expression system: Not provided
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2932 nucleotides
Theoretical weight: 951.06 KDa
Source organism: Listeria innocua
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 116 nucleotides
Theoretical weight: 37.3 KDa
Source organism: Listeria innocua
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:

Experiments and Validation Details

Entry percentile scores
Resolution:
Relevant EMDB volumes: EMD-42557
Expression systems:
  • Escherichia coli HB101
  • Not provided