› 7a18

X-ray diffraction
3.4Å resolution

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155891 (preferred)
Entry contents:
26 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (28 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 29.53 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ9 (Residues: 2-272; Coverage: 99%)
Gene names: DR_0314, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 206 amino acids
Theoretical weight: 22.03 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-206; Coverage: 98%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 195 amino acids
Theoretical weight: 21.15 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXK1 (Residues: 2-196; Coverage: 95%)
Gene names: DR_0312, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: D
Molecule details ›
Chain: D
Length: 176 amino acids
Theoretical weight: 19.83 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ0 (Residues: 2-177; Coverage: 98%)
Gene names: DR_0323, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: E
Molecule details ›
Chain: E
Length: 171 amino acids
Theoretical weight: 18.27 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSL3 (Residues: 5-175; Coverage: 92%)
Gene names: DR_2111, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: G
Molecule details ›
Chain: G
Length: 142 amino acids
Theoretical weight: 15.84 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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 R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ2 (Residues: 1-134; Coverage: 100%)
Gene names: DR_0321, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: I
Molecule details ›
Chain: I
Length: 137 amino acids
Theoretical weight: 14.8 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSK9 (Residues: 1-137; Coverage: 88%)
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: 134 amino acids
Theoretical weight: 15.34 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ5 (Residues: 5-138; Coverage: 95%)
Gene names: DR_0318, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: K
Molecule details ›
Chain: K
Length: 115 amino acids
Theoretical weight: 12.83 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSJ5 (Residues: 1-115; Coverage: 99%)
Gene names: DR_2129, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: L
Molecule details ›
Chain: L
Length: 104 amino acids
Theoretical weight: 11.1 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSL2 (Residues: 8-111; Coverage: 91%)
Gene names: DR_2112, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: M
Molecule details ›
Chain: M
Length: 118 amino acids
Theoretical weight: 13.45 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RWB4 (Residues: 2-119; Coverage: 71%)
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 R1 = ATCC 13939 = DSM 20539
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: 98 amino acids
Theoretical weight: 10.89 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RY64 (Residues: 1-98; Coverage: 98%)
Gene names: DR_0086, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 129 amino acids
Theoretical weight: 14.66 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ7 (Residues: 6-134; Coverage: 96%)
Gene names: DR_0316, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: Q
Molecule details ›
Chain: Q
Length: 93 amino acids
Theoretical weight: 10.34 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXK0 (Residues: 2-94; Coverage: 98%)
Gene names: DR_0313, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: R
Molecule details ›
Chain: R
Length: 110 amino acids
Theoretical weight: 11.77 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ1 (Residues: 4-113; Coverage: 96%)
Gene names: DR_0322, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: S
Molecule details ›
Chain: S
Length: 175 amino acids
Theoretical weight: 19.18 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RX88 (Residues: 1-175; Coverage: 74%)
Gene names: DR_0427, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chain: T
Molecule details ›
Chain: T
Length: 72 amino acids
Theoretical weight: 7.71 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RY65 (Residues: 12-83; Coverage: 79%)
Gene names: DR_0085, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: U
Molecule details ›
Chain: U
Length: 74 amino acids
Theoretical weight: 8.15 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RRG8 (Residues: 6-79; Coverage: 91%)
Gene names: DR_2524, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: V
Molecule details ›
Chain: V
Length: 54 amino acids
Theoretical weight: 6.26 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ4 (Residues: 13-66; Coverage: 81%)
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 R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSL0 (Residues: 1-55; Coverage: 100%)
Gene names: DR_2114, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: Z
Molecule details ›
Chain: Z
Length: 57 amino acids
Theoretical weight: 6.51 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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: 49 amino acids
Theoretical weight: 5.77 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSS4 (Residues: 6-54; Coverage: 89%)
Gene names: DR_2049, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
Chain: 2
Length: 46 amino acids
Theoretical weight: 5.5 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSH2 (Residues: 1-46; Coverage: 98%)
Gene names: DR_2152, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 63 amino acids
Theoretical weight: 7.13 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RSW6 (Residues: 2-64; Coverage: 96%)
Gene names: DR_2005, rpmI
Sequence domains: Ribosomal protein L35
RNA (2699-MER) Chain: X
Molecule details ›
Chain: X
Length: 2699 nucleotides
Theoretical weight: 875.1 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
RNA (122-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 122 nucleotides
Theoretical weight: 39.28 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MIV 1 x MIV
Ligand MG 277 x MG
Ligand SPD 7 x SPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: I222
Unit cell:
a: 169.59Å b: 410.128Å c: 690.477Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.285 0.284 0.318

Quick links

Citations

1 review citation

Success stories of natural product-derived compounds from plants as multidrug resistance modulators in microorganisms.
Zhai et al. (2023)
4 other articles

1 mention without citation

Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida.
Breiner-Goldstein et al. (2021)