PDBe 2zjp

X-ray diffraction
3.7Å resolution

Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
Entry contents:
29 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (31 distinct):
50S ribosomal protein L33 Chain: 1
Molecule details ›
Chain: 1
Length: 55 amino acids
Theoretical weight: 6.37 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSS4 (Residues: 1-55; Coverage: 100%)
Gene names: DR_2049, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chain: 2
Molecule details ›
Chain: 2
Length: 47 amino acids
Theoretical weight: 5.63 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSH2 (Residues: 1-47; Coverage: 100%)
Gene names: DR_2152, rpmH
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chain: 3
Molecule details ›
Chain: 3
Length: 66 amino acids
Theoretical weight: 7.45 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSW6 (Residues: 1-66; Coverage: 100%)
Gene names: DR_2005, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chain: 4
Molecule details ›
Chain: 4
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSK0 (Residues: 1-37; Coverage: 100%)
Gene names: DR_2124, rpmJ
Sequence domains: Ribosomal protein L36
Nosiheptide Chain: 5
Molecule details ›
Chain: 5
Length: 13 amino acids
Theoretical weight: 1.2 KDa
Source organism: Streptomyces actuosus
UniProt:
  • Canonical: NEW C6FX52 (Residues: 38-50; Coverage: 26%)
Gene name: nosM
50S ribosomal protein L2 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 29.98 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ9 (Residues: 2-275; Coverage: 100%)
Gene names: DR_0314, rplB
Sequence domains:
Structure domains: Nucleic acid-binding proteins
50S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 211 amino acids
Theoretical weight: 22.48 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXK2 (Residues: 1-211; Coverage: 100%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chain: C
Molecule details ›
Chain: C
Length: 205 amino acids
Theoretical weight: 22.31 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXK1 (Residues: 1-205; Coverage: 100%)
Gene names: DR_0312, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chain: D
Molecule details ›
Chain: D
Length: 180 amino acids
Theoretical weight: 20.38 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ0 (Residues: 1-180; Coverage: 100%)
Gene names: DR_0323, rplE
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
50S ribosomal protein L6 Chain: E
Molecule details ›
Chain: E
Length: 185 amino acids
Theoretical weight: 19.61 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSL3 (Residues: 1-185; Coverage: 100%)
Gene names: DR_2111, rplF
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
50S ribosomal protein L11 Chain: F
Molecule details ›
Chain: F
Length: 144 amino acids
Theoretical weight: 14.89 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSS7 (Residues: 1-144; Coverage: 100%)
Gene names: DR_2046, rplK
Sequence domains:
Structure domains:
50S ribosomal protein L13 Chain: G
Molecule details ›
Chain: G
Length: 174 amino acids
Theoretical weight: 19.22 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXY1 (Residues: 1-174; Coverage: 100%)
Gene names: DR_0174, rplM
Sequence domains: Ribosomal protein L13
Structure domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: H
Molecule details ›
Chain: H
Length: 134 amino acids
Theoretical weight: 14.26 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ2 (Residues: 1-134; Coverage: 100%)
Gene names: DR_0321, rplN
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
50S ribosomal protein L15 Chain: I
Molecule details ›
Chain: I
Length: 156 amino acids
Theoretical weight: 16.89 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSK9 (Residues: 1-156; Coverage: 100%)
Gene names: DR_2115, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 16.26 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ5 (Residues: 1-141; Coverage: 100%)
Gene names: DR_0318, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
50S ribosomal protein L17 Chain: K
Molecule details ›
Chain: K
Length: 116 amino acids
Theoretical weight: 12.93 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSJ5 (Residues: 1-116; Coverage: 100%)
Gene names: DR_2129, rplQ
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
50S ribosomal protein L18 Chain: L
Molecule details ›
Chain: L
Length: 114 amino acids
Theoretical weight: 12.16 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW 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
50S ribosomal protein L19 Chain: M
Molecule details ›
Chain: M
Length: 166 amino acids
Theoretical weight: 18.35 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RWB4 (Residues: 1-166; Coverage: 100%)
Gene names: DR_0755, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chain: N
Molecule details ›
Chain: N
Length: 118 amino acids
Theoretical weight: 13.99 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RSW7 (Residues: 1-118; Coverage: 100%)
Gene names: DR_2004, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chain: O
Molecule details ›
Chain: O
Length: 100 amino acids
Theoretical weight: 11.17 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RY64 (Residues: 1-100; Coverage: 100%)
Gene names: DR_0086, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chain: P
Molecule details ›
Chain: P
Length: 134 amino acids
Theoretical weight: 15.19 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ7 (Residues: 1-134; Coverage: 100%)
Gene names: DR_0316, rplV
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
50S ribosomal protein L23 Chain: Q
Molecule details ›
Chain: Q
Length: 95 amino acids
Theoretical weight: 10.54 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXK0 (Residues: 1-95; Coverage: 100%)
Gene names: DR_0313, rplW
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
50S ribosomal protein L24 Chain: R
Molecule details ›
Chain: R
Length: 115 amino acids
Theoretical weight: 12.38 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ1 (Residues: 1-115; Coverage: 100%)
Gene names: DR_0322, rplX
Sequence domains:
50S ribosomal protein L25 Chain: S
Molecule details ›
Chain: S
Length: 237 amino acids
Theoretical weight: 25.42 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RX88 (Residues: 1-237; Coverage: 100%)
Gene names: DR_0427, ctc, rplY
Sequence domains:
Structure domains:
50S ribosomal protein L27 Chain: T
Molecule details ›
Chain: T
Length: 91 amino acids
Theoretical weight: 9.61 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RY65 (Residues: 1-91; Coverage: 100%)
Gene names: DR_0085, rpmA
Sequence domains: Ribosomal L27 protein
50S ribosomal protein L28 Chain: U
Molecule details ›
Chain: U
Length: 81 amino acids
Theoretical weight: 8.98 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RRG8 (Residues: 1-81; Coverage: 100%)
Gene names: DR_2524, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chain: V
Molecule details ›
Chain: V
Length: 67 amino acids
Theoretical weight: 7.77 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW Q9RXJ4 (Residues: 1-67; Coverage: 100%)
Gene names: DR_0319, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chain: W
Molecule details ›
Chain: W
Length: 55 amino acids
Theoretical weight: 6.08 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW 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
50S ribosomal protein L32 Chain: Y
Molecule details ›
Chain: Y
Length: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: NEW P49228 (Residues: 1-60; Coverage: 100%)
Gene names: DR_2366, rpmF
Sequence domains: Ribosomal L32p protein family
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: Z
Molecule details ›
Chain: Z
Length: 123 nucleotides
Theoretical weight: 39.61 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA, ESRF BEAMLINE ID29
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
0.3 0.3 0.34