› 8uu8

Electron Microscopy
3.1Å resolution

Cryo-EM structure of the Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-C)

Released:
DOI: 10.2210/pdb8uu8/pdb
PDB entry 8uu8 coloured by chain, front view.
PDB entry 8uu8 coloured by chain, side view.
PDB entry 8uu8 coloured by chain, top view.
Source organisms:
Primary publication:
Mechanistic insights into the alternative ribosome recycling by HflXr.
Seely SM, Basu RS, Gagnon MG
OpenAccess logo Nucleic Acids Res (2024)
PMID: 38407413
Related structures: EMD-42571

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
PDBe Complex ID:
PDB-CPX-268749 (preferred)
Entry contents:
49 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (54 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
UniProt:
  • Canonical: A0A0U4VSU9 (Residues: 1-218; Coverage: 100%)
Gene names: HB837_08100, JJJ81_11355, rpsC
Sequence domains:
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
UniProt:
  • Canonical: A0A0U4VSJ3 (Residues: 1-167; Coverage: 100%)
Gene names: HB837_08045, JJJ81_11410, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 97 amino acids
Theoretical weight: 11.51 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A7X0WKH5 (Residues: 1-97; Coverage: 100%)
Gene names: HB837_09480, JJJ81_09985, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 17.85 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JPE1 (Residues: 1-156; Coverage: 100%)
Gene names: HB837_08270, JJJ81_11185, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 132 amino acids
Theoretical weight: 14.67 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5A6U3 (Residues: 1-132; Coverage: 100%)
Gene names: HB837_08060, JJJ81_11395, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 130 amino acids
Theoretical weight: 14.47 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5ADS9 (Residues: 1-130; Coverage: 100%)
Gene names: HB837_07950, JJJ81_11505, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 102 amino acids
Theoretical weight: 11.7 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5A730 (Residues: 1-102; Coverage: 100%)
Gene names: HB837_08135, JJJ81_11320, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.81 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AP31 (Residues: 1-129; Coverage: 100%)
Gene names: HB837_08005, JJJ81_11450, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 137 amino acids
Theoretical weight: 15.22 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JM56 (Residues: 1-137; Coverage: 100%)
Gene names: HB837_08275, JJJ81_11180, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 121 amino acids
Theoretical weight: 13.74 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5ARJ0 (Residues: 1-121; Coverage: 100%)
Gene names: HB837_08010, JJJ81_11445, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: n
Molecule details ›
Chain: n
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AGZ1 (Residues: 1-61; Coverage: 100%)
Gene names: HB837_08065, JJJ81_11390, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.66 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JLK4 (Residues: 1-89; Coverage: 100%)
Gene names: HB837_01100, JJJ81_07850, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 90 amino acids
Theoretical weight: 10.4 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A6B0JQE1 (Residues: 1-90; Coverage: 100%)
Gene names: HB837_05950, JJJ81_05055, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 87 amino acids
Theoretical weight: 10.06 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5ADR4 (Residues: 1-87; Coverage: 100%)
Gene names: HB837_08085, JJJ81_11370, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 79 amino acids
Theoretical weight: 9.12 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JK14 (Residues: 1-79; Coverage: 100%)
Gene names: HB837_09490, JJJ81_09975, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 92 amino acids
Theoretical weight: 10.5 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4VSH5 (Residues: 1-92; Coverage: 100%)
Gene names: HB837_08110, JJJ81_11345, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 84 amino acids
Theoretical weight: 9.19 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JML5 (Residues: 1-84; Coverage: 100%)
Gene names: HB837_01985, JJJ81_08600, rpsT
Sequence domains: Ribosomal protein S20
GTPase HflX Chain: v
Molecule details ›
Chain: v
Length: 418 amino acids
Theoretical weight: 47.61 KDa
Source organism: Listeria monocytogenes EGD-e
UniProt:
  • Canonical: Q8Y8Y0 (Residues: 1-418; Coverage: 100%)
Gene names: hflX, lmo0762
Sequence domains:
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 277 amino acids
Theoretical weight: 30.57 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5A742 (Residues: 1-277; Coverage: 100%)
Gene names: HB837_08115, JJJ81_11340, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.88 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5ADD0 (Residues: 1-209; Coverage: 100%)
Gene names: HB837_08130, JJJ81_11325, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 207 amino acids
Theoretical weight: 22.64 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4VSH7 (Residues: 1-207; Coverage: 100%)
Gene names: JJJ81_11330, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.02 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AWX6 (Residues: 1-179; Coverage: 100%)
Gene names: HB837_08070, JJJ81_11385, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 178 amino acids
Theoretical weight: 19.43 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5ALU0 (Residues: 1-178; Coverage: 100%)
Gene names: HB837_08055, JJJ81_11400, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL10 Chain: I
Molecule details ›
Chain: I
Length: 166 amino acids
Theoretical weight: 17.72 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5A6T9 (Residues: 1-166; Coverage: 100%)
Gene names: HB837_12435, JJJ81_04825, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11 Chain: H
Molecule details ›
Chain: H
Length: 141 amino acids
Theoretical weight: 14.88 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JML6 (Residues: 1-141; Coverage: 100%)
Gene names: HB837_12425, JJJ81_04835, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: L
Molecule details ›
Chain: L
Length: 145 amino acids
Theoretical weight: 16.23 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AGN0 (Residues: 1-145; Coverage: 100%)
Gene names: JJJ81_11500, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: M
Molecule details ›
Chain: M
Length: 122 amino acids
Theoretical weight: 13.25 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AP82 (Residues: 1-122; Coverage: 100%)
Gene names: HB837_08080, JJJ81_11375, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: N
Molecule details ›
Chain: N
Length: 146 amino acids
Theoretical weight: 15.83 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5A6S7 (Residues: 1-146; Coverage: 100%)
Gene names: HB837_08035, JJJ81_11420, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: O
Molecule details ›
Chain: O
Length: 144 amino acids
Theoretical weight: 16.17 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4VSU8 (Residues: 1-144; Coverage: 100%)
Gene names: HB837_08095, JJJ81_11360, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: P
Molecule details ›
Chain: P
Length: 135 amino acids
Theoretical weight: 15.24 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4VSW3 (Residues: 1-135; Coverage: 99%)
Gene names: HB837_07995, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: Q
Molecule details ›
Chain: Q
Length: 119 amino acids
Theoretical weight: 13.11 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AR65 (Residues: 1-119; Coverage: 100%)
Gene names: JJJ81_11405, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: R
Molecule details ›
Chain: R
Length: 114 amino acids
Theoretical weight: 13.09 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A6B0JQF2 (Residues: 1-114; Coverage: 100%)
Gene names: HB837_05900, JJJ81_05005, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: S
Molecule details ›
Chain: S
Length: 119 amino acids
Theoretical weight: 13.72 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JH71 (Residues: 1-119; Coverage: 100%)
Gene names: HB837_05865, JJJ81_04970, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: T
Molecule details ›
Chain: T
Length: 102 amino acids
Theoretical weight: 11.22 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AD18 (Residues: 1-102; Coverage: 100%)
Gene names: HB837_02300, JJJ81_08915, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: U
Molecule details ›
Chain: U
Length: 118 amino acids
Theoretical weight: 12.9 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5ANW2 (Residues: 1-118; Coverage: 100%)
Gene names: HB837_08105, JJJ81_11350, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: V
Molecule details ›
Chain: V
Length: 94 amino acids
Theoretical weight: 10.95 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4MTC5 (Residues: 1-94; Coverage: 100%)
Gene names: HB837_08120, JJJ81_11335, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: W
Molecule details ›
Chain: W
Length: 103 amino acids
Theoretical weight: 11.22 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AD05 (Residues: 1-103; Coverage: 100%)
Gene names: HB837_08075, JJJ81_11380, rplX
Sequence domains:
Large ribosomal subunit protein bL27 Chain: Y
Molecule details ›
Chain: Y
Length: 96 amino acids
Theoretical weight: 10.57 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JMC7 (Residues: 1-96; Coverage: 100%)
Gene names: HB837_02290, JJJ81_08905, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: Z
Molecule details ›
Chain: Z
Length: 62 amino acids
Theoretical weight: 7.01 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JJV9 (Residues: 1-62; Coverage: 100%)
Gene names: HB837_06045, JJJ81_05150, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: 1
Molecule details ›
Chain: 1
Length: 63 amino acids
Theoretical weight: 7.41 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AGL9 (Residues: 1-63; Coverage: 100%)
Gene names: HB837_08090, JJJ81_11365, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: 2
Molecule details ›
Chain: 2
Length: 59 amino acids
Theoretical weight: 6.5 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4VSJ1 (Residues: 1-59; Coverage: 100%)
Gene names: HB837_08040, JJJ81_11415, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31B Chain: 3
Molecule details ›
Chain: 3
Length: 81 amino acids
Theoretical weight: 9.27 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U4MT39 (Residues: 1-81; Coverage: 100%)
Gene names: HB837_10690, JJJ81_12465, rpmE2, rpsU
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: 4
Molecule details ›
Chain: 4
Length: 57 amino acids
Theoretical weight: 6.53 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JNN0 (Residues: 1-57; Coverage: 100%)
Gene names: HB837_07190, JJJ81_06260, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 5
Molecule details ›
Chain: 5
Length: 49 amino acids
Theoretical weight: 6.02 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JRA4 (Residues: 1-49; Coverage: 100%)
Gene names: HB837_01125, JJJ81_07875, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 6
Molecule details ›
Chain: 6
Length: 44 amino acids
Theoretical weight: 5.32 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JKZ6 (Residues: 1-44; Coverage: 100%)
Gene names: HB837_09275, JJJ81_10175, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 7
Molecule details ›
Chain: 7
Length: 66 amino acids
Theoretical weight: 7.75 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A660JIB9 (Residues: 1-66; Coverage: 100%)
Gene names: HB837_05870, JJJ81_04975, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 8
Molecule details ›
Chain: 8
Length: 37 amino acids
Theoretical weight: 4.34 KDa
Source organism: Listeria innocua
UniProt:
  • Canonical: A0A0U5AM58 (Residues: 1-37; Coverage: 100%)
Gene names: HB837_08015, JJJ81_11440, rpmJ
Sequence domains: Ribosomal protein L36
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1550 nucleotides
Theoretical weight: 501.95 KDa
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
Sequence domains: tRNA
F-Stop mRNA Chain: w
Molecule details ›
Chain: w
Length: 21 nucleotides
Theoretical weight: 6.79 KDa
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2932 nucleotides
Theoretical weight: 951.06 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 116 nucleotides
Theoretical weight: 37.3 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 423 x MG
Ligand ZN 4 x ZN
Ligand GCP 1 x GCP
5 modified residues:
Ligand 4SU 1 x 4SU
Ligand PSU 3 x PSU
Ligand MIA 1 x MIA
Ligand G7M 1 x G7M
Ligand 5MU 1 x 5MU

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-42571

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