› 2zjq

X-ray diffraction
3.3Å resolution

Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit

Released:
DOI: 10.2210/pdb2zjq/pdb
PDB entry 2zjq coloured by chain, front view.
PDB entry 2zjq coloured by chain, side view.
PDB entry 2zjq coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P
Mol Cell 30 26-38 (2008)
PMID: 18406324

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155875 (preferred)
Entry contents:
29 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (31 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 29.98 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ9 (Residues: 2-275; Coverage: 100%)
Gene names: DR_0314, rplB
Sequence domains:
Structure domains: Nucleic acid-binding proteins
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 211 amino acids
Theoretical weight: 22.48 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-211; Coverage: 100%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 205 amino acids
Theoretical weight: 22.31 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK1 (Residues: 1-205; Coverage: 100%)
Gene names: DR_0312, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: D
Molecule details ›
Chain: D
Length: 180 amino acids
Theoretical weight: 20.38 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ0 (Residues: 1-180; Coverage: 100%)
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: 185 amino acids
Theoretical weight: 19.61 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSL3 (Residues: 1-185; Coverage: 100%)
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: 14.89 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: 174 amino acids
Theoretical weight: 19.22 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXY1 (Residues: 1-174; Coverage: 100%)
Gene names: DR_0174, rplM
Sequence domains: Ribosomal protein L13
Structure 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: 156 amino acids
Theoretical weight: 16.89 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSK9 (Residues: 1-156; Coverage: 100%)
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: 142 amino acids
Theoretical weight: 16.26 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ5 (Residues: 1-141; Coverage: 100%)
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: 116 amino acids
Theoretical weight: 12.93 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSJ5 (Residues: 1-116; Coverage: 100%)
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: 114 amino acids
Theoretical weight: 12.16 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSL2 (Residues: 1-114; Coverage: 100%)
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: 166 amino acids
Theoretical weight: 18.35 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RWB4 (Residues: 1-166; Coverage: 100%)
Gene names: DR_0755, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: N
Molecule details ›
Chain: N
Length: 118 amino acids
Theoretical weight: 13.99 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSW7 (Residues: 1-118; Coverage: 100%)
Gene names: DR_2004, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: O
Molecule details ›
Chain: O
Length: 100 amino acids
Theoretical weight: 11.17 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RY64 (Residues: 1-100; Coverage: 100%)
Gene names: DR_0086, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 134 amino acids
Theoretical weight: 15.19 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ7 (Residues: 1-134; Coverage: 100%)
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: 95 amino acids
Theoretical weight: 10.54 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK0 (Residues: 1-95; Coverage: 100%)
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: 115 amino acids
Theoretical weight: 12.38 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ1 (Residues: 1-115; Coverage: 100%)
Gene names: DR_0322, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: S
Molecule details ›
Chain: S
Length: 237 amino acids
Theoretical weight: 25.42 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RX88 (Residues: 1-237; Coverage: 100%)
Gene names: DR_0427, ctc, rplY
Sequence domains:
Structure domains:
Large ribosomal subunit protein bL27 Chain: T
Molecule details ›
Chain: T
Length: 91 amino acids
Theoretical weight: 9.61 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RY65 (Residues: 1-91; Coverage: 100%)
Gene names: DR_0085, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: U
Molecule details ›
Chain: U
Length: 81 amino acids
Theoretical weight: 8.98 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RRG8 (Residues: 1-81; Coverage: 100%)
Gene names: DR_2524, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: V
Molecule details ›
Chain: V
Length: 67 amino acids
Theoretical weight: 7.77 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ4 (Residues: 1-67; Coverage: 100%)
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: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: P49228 (Residues: 1-60; Coverage: 100%)
Gene names: DR_2366, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 1
Molecule details ›
Chain: 1
Length: 55 amino acids
Theoretical weight: 6.37 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSS4 (Residues: 1-55; Coverage: 100%)
Gene names: DR_2049, rpmG
Sequence 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
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 66 amino acids
Theoretical weight: 7.45 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSW6 (Residues: 1-66; Coverage: 100%)
Gene names: DR_2005, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 4
Molecule details ›
Chain: 4
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RSK0 (Residues: 1-37; Coverage: 100%)
Gene names: DR_2124, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein bL12 Chain: 5
Molecule details ›
Chain: 5
Length: 122 amino acids
Theoretical weight: 12.64 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RST0 (Residues: 1-122; Coverage: 100%)
Gene names: DR_2043, rplL
Sequence domains:
23S ribosomal RNA Chain: X
Molecule details ›
Chain: X
Length: 2880 nucleotides
Theoretical weight: 933.41 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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29, SLS BEAMLINE X06SA
Spacegroup: I222
Unit cell:
a: 169.9Å b: 408.9Å c: 694.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.302 not available 0.339

Quick links

Citations

42 review citations

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
Arnison et al. (2013)
41 more

2 mentions without citation

Charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms.
Fedyukina et al. (2014)
1 more