› 5dm7

X-ray diffraction
3Å resolution

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A

Released:
DOI: 10.2210/pdb5dm7/pdb
PDB entry 5dm7 coloured by chain, front view.
PDB entry 5dm7 coloured by chain, side view.
PDB entry 5dm7 coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
Kaminishi T, Schedlbauer A, Fabbretti A, Brandi L, Ochoa-Lizarralde B, He CG, Milón P, Connell SR, Gualerzi CO, Fucini P
Nucleic Acids Res 43 10015-25 (2015)
PMID: 26464437

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155884 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL1 Chain: 0
Molecule details ›
Chain: 0
Length: 224 amino acids
Theoretical weight: 23.51 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSS8 (Residues: 6-229; Coverage: 96%)
Gene names: DR_2045, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Structure domains:
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 29.92 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ9 (Residues: 2-275; Coverage: 100%)
Gene names: DR_0314, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 205 amino acids
Theoretical weight: 21.96 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-205; Coverage: 97%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 197 amino acids
Theoretical weight: 21.41 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK1 (Residues: 2-198; Coverage: 96%)
Gene names: DR_0312, rplD
Sequence domains: Ribosomal protein L4/L1 family
Structure domains: Ribosomal Protein L4; Chain: A;
Large ribosomal subunit protein uL5 Chain: D
Molecule details ›
Chain: D
Length: 177 amino acids
Theoretical weight: 19.99 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ0 (Residues: 3-179; Coverage: 98%)
Gene names: DR_0323, rplE
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
Large ribosomal subunit protein uL6 Chain: E
Molecule details ›
Chain: E
Length: 171 amino acids
Theoretical weight: 18.27 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSL3 (Residues: 5-175; Coverage: 92%)
Gene names: DR_2111, rplF
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein uL11 Chain: F
Molecule details ›
Chain: F
Length: 144 amino acids
Theoretical weight: 14.95 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSS7 (Residues: 1-144; Coverage: 100%)
Gene names: DR_2046, rplK
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL13 Chain: G
Molecule details ›
Chain: G
Length: 142 amino acids
Theoretical weight: 15.84 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXY1 (Residues: 30-171; Coverage: 82%)
Gene names: DR_0174, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: H
Molecule details ›
Chain: H
Length: 134 amino acids
Theoretical weight: 14.26 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ2 (Residues: 1-134; Coverage: 100%)
Gene names: DR_0321, rplN
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15 Chain: I
Molecule details ›
Chain: I
Length: 141 amino acids
Theoretical weight: 15.18 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSK9 (Residues: 4-144; Coverage: 90%)
Gene names: DR_2115, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: J
Molecule details ›
Chain: J
Length: 136 amino acids
Theoretical weight: 15.54 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ5 (Residues: 5-140; Coverage: 97%)
Gene names: DR_0318, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL17 Chain: K
Molecule details ›
Chain: K
Length: 113 amino acids
Theoretical weight: 12.54 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSJ5 (Residues: 3-115; Coverage: 97%)
Gene names: DR_2129, rplQ
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: L
Molecule details ›
Chain: L
Length: 104 amino acids
Theoretical weight: 11.07 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSL2 (Residues: 8-111; Coverage: 91%)
Gene names: DR_2112, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein bL19 Chain: M
Molecule details ›
Chain: M
Length: 109 amino acids
Theoretical weight: 12.29 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RWB4 (Residues: 2-115; Coverage: 66%)
Gene names: DR_0755, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: N
Molecule details ›
Chain: N
Length: 117 amino acids
Theoretical weight: 13.86 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSW7 (Residues: 2-118; Coverage: 99%)
Gene names: DR_2004, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: O
Molecule details ›
Chain: O
Length: 94 amino acids
Theoretical weight: 10.52 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RY64 (Residues: 5-98; Coverage: 94%)
Gene names: DR_0086, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 127 amino acids
Theoretical weight: 14.43 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ7 (Residues: 8-134; Coverage: 95%)
Gene names: DR_0316, rplV
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: Q
Molecule details ›
Chain: Q
Length: 93 amino acids
Theoretical weight: 10.34 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK0 (Residues: 2-94; Coverage: 98%)
Gene names: DR_0313, rplW
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: R
Molecule details ›
Chain: R
Length: 110 amino acids
Theoretical weight: 11.77 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ1 (Residues: 4-113; Coverage: 96%)
Gene names: DR_0322, rplX
Sequence domains:
Structure domains: SH3 type barrels.
Large ribosomal subunit protein bL25 Chain: S
Molecule details ›
Chain: S
Length: 175 amino acids
Theoretical weight: 19.18 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RX88 (Residues: 1-175; Coverage: 74%)
Gene names: DR_0427, ctc, rplY
Sequence domains:
Structure domains:
Large ribosomal subunit protein bL27 Chain: T
Molecule details ›
Chain: T
Length: 84 amino acids
Theoretical weight: 8.89 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RY65 (Residues: 2-85; Coverage: 92%)
Gene names: DR_0085, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: U
Molecule details ›
Chain: U
Length: 72 amino acids
Theoretical weight: 7.87 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RRG8 (Residues: 8-79; Coverage: 89%)
Gene names: DR_2524, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: V
Molecule details ›
Chain: V
Length: 66 amino acids
Theoretical weight: 7.65 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ4 (Residues: 1-66; Coverage: 99%)
Gene names: DR_0319, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: W
Molecule details ›
Chain: W
Length: 55 amino acids
Theoretical weight: 6.08 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSL0 (Residues: 1-55; Coverage: 100%)
Gene names: DR_2114, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Structure domains: Ribosomal protein L30, ferredoxin-like fold domain
Large ribosomal subunit protein bL32 Chain: Z
Molecule details ›
Chain: Z
Length: 57 amino acids
Theoretical weight: 6.51 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: P49228 (Residues: 3-59; Coverage: 95%)
Gene names: DR_2366, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 1
Molecule details ›
Chain: 1
Length: 54 amino acids
Theoretical weight: 5.74 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSS4 (Residues: 2-50; Coverage: 89%)
Gene names: DR_2049, rpmG
Sequence domains: Ribosomal protein L33
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
Chain: 2
Length: 47 amino acids
Theoretical weight: 5.63 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSH2 (Residues: 1-47; Coverage: 100%)
Gene names: DR_2152, rpmH
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 65 amino acids
Theoretical weight: 7.32 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSW6 (Residues: 2-66; Coverage: 99%)
Gene names: DR_2005, rpmI
Sequence domains: Ribosomal protein L35
Structure domains: Factor Xa Inhibitor
23S ribosomal RNA Chain: X
Molecule details ›
Chain: X
Length: 2881 nucleotides
Theoretical weight: 933.75 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: Y
Molecule details ›
Chain: Y
Length: 122 nucleotides
Theoretical weight: 39.28 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 186 x MG
Ligand HGR 1 x HGR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: I222
Unit cell:
a: 169.82Å b: 411.54Å c: 695.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.286 0.284 0.326

Quick links

Citations

9 citation in other articles

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Melnikov et al. (2016)
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4 mentions without citation

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Leonarski et al. (2017)
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