› 3cma

X-ray diffraction
2.8Å resolution

The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui

Released:
DOI: 10.2210/pdb3cma/pdb
PDB 3cma coloured by chain and viewed from the front.
PDB 3cma coloured by chain and viewed from the side.
PDB 3cma coloured by chain and viewed from the top.
Source organism: Haloarcula marismortui
Primary publication:
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
Simonović M, Steitz TA
RNA 14 2372-8 (2008)
PMID: 18818369

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 33-mer (preferred)
Entry contents:
29 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (33 distinct):
50S ribosomal protein L2 Chain: A
Molecule details ›
Chain: A
Length: 240 amino acids
Theoretical weight: 25.35 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20276 (Residues: 1-240; Coverage: 100%)
Gene names: rpl2, rrnAC1608
Sequence domains:
Structure domains:
50S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 338 amino acids
Theoretical weight: 37.4 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20279 (Residues: 1-338; Coverage: 100%)
Gene names: rpl3, rrnAC1611
Sequence domains: Ribosomal protein L3
Structure domains:
50S ribosomal protein L4 Chain: C
Molecule details ›
Chain: C
Length: 246 amino acids
Theoretical weight: 26.46 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12735 (Residues: 1-246; Coverage: 100%)
Gene names: rpl4, rrnAC1610
Sequence domains: Ribosomal protein L4/L1 family
Structure domains: Ribosomal Protein L4; Chain: A;
50S ribosomal protein L5 Chain: D
Molecule details ›
Chain: D
Length: 177 amino acids
Theoretical weight: 19.55 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14124 (Residues: 1-177; Coverage: 100%)
Gene names: rpl5, rrnAC1598
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
50S ribosomal protein L6 Chain: E
Molecule details ›
Chain: E
Length: 178 amino acids
Theoretical weight: 19.96 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14135 (Residues: 1-178; Coverage: 100%)
Gene names: rpl6, rrnAC1596
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
50S ribosomal protein L7Ae Chain: F
Molecule details ›
Chain: F
Length: 120 amino acids
Theoretical weight: 12.79 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12743 (Residues: 1-120; Coverage: 100%)
Gene names: rpl7ae, rrnAC0103
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
50S ribosomal protein L10 Chain: G
Molecule details ›
Chain: G
Length: 348 amino acids
Theoretical weight: 37.17 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P15825 (Residues: 1-348; Coverage: 100%)
Gene names: rpl10, rpl10e, rplP0, rrnAC1417
Sequence domains:
50S ribosomal protein L10e Chain: H
Molecule details ›
Chain: H
Length: 177 amino acids
Theoretical weight: 19.94 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60617 (Residues: 1-177; Coverage: 100%)
Gene names: rpl10e, rrnAC2357
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
50S ribosomal protein L11 Chain: I
Molecule details ›
Chain: I
Length: 162 amino acids
Theoretical weight: 17.1 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14122 (Residues: 1-162; Coverage: 100%)
Gene names: rpl11, rrnAC1414
Sequence domains:
Structure domains: Ribosomal protein L11, C-terminal domain
50S ribosomal protein L13 Chain: J
Molecule details ›
Chain: J
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P29198 (Residues: 1-145; Coverage: 100%)
Gene names: rpl13, rrnAC0065
Sequence domains: Ribosomal protein L13
Structure domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: K
Molecule details ›
Chain: K
Length: 132 amino acids
Theoretical weight: 14.22 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22450 (Residues: 1-132; Coverage: 100%)
Gene names: rpl14, rrnAC1602
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
50S ribosomal protein L15 Chain: L
Molecule details ›
Chain: L
Length: 165 amino acids
Theoretical weight: 18.01 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12737 (Residues: 1-165; Coverage: 100%)
Gene names: rpl15, rrnAC1590
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Structure domains:
50S ribosomal protein L15e Chain: M
Molecule details ›
Chain: M
Length: 196 amino acids
Theoretical weight: 22.4 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60618 (Residues: 1-196; Coverage: 100%)
Gene names: rpl15e, rrnAC2065
Sequence domains: Ribosomal L15
Structure domains: Ribosomal protein l15e
50S ribosomal protein L18 Chain: N
Molecule details ›
Chain: N
Length: 187 amino acids
Theoretical weight: 20.64 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14123 (Residues: 1-187; Coverage: 100%)
Gene names: rpl18, rrnAC1593
Sequence domains: Ribosomal large subunit proteins 60S L5, and 50S L18
Structure domains: Nucleotidyltransferase; domain 5
50S ribosomal protein L18e Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 12.44 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12733 (Residues: 1-116; Coverage: 100%)
Gene names: rpl18e, rrnAC0064
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Structure domains: Ribosomal Protein L15; Chain: K; domain 2
50S ribosomal protein L19e Chain: P
Molecule details ›
Chain: P
Length: 149 amino acids
Theoretical weight: 16.8 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14119 (Residues: 1-149; Coverage: 100%)
Gene names: rpl19e, rrnAC1594
Sequence domains: Ribosomal protein L19e
Structure domains:
50S ribosomal protein L21e Chain: Q
Molecule details ›
Chain: Q
Length: 96 amino acids
Theoretical weight: 10.57 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12734 (Residues: 1-96; Coverage: 100%)
Gene names: rpl21e, rrnAC0260
Sequence domains: Ribosomal protein L21e
Structure domains: Ribosomal protein L21
50S ribosomal protein L22 Chain: R
Molecule details ›
Chain: R
Length: 155 amino acids
Theoretical weight: 16.97 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10970 (Residues: 1-155; Coverage: 100%)
Gene names: rpl22, rrnAC1606
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
50S ribosomal protein L23 Chain: S
Molecule details ›
Chain: S
Length: 85 amino acids
Theoretical weight: 9.61 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12732 (Residues: 1-85; Coverage: 100%)
Gene names: rpl23, rrnAC1609
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
50S ribosomal protein L24 Chain: T
Molecule details ›
Chain: T
Length: 120 amino acids
Theoretical weight: 13.67 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10972 (Residues: 1-120; Coverage: 100%)
Gene names: rpl24, rrnAC1601
Sequence domains:
Structure domains: SH3 type barrels.
50S ribosomal protein L24e Chain: U
Molecule details ›
Chain: U
Length: 67 amino acids
Theoretical weight: 7.36 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14116 (Residues: 1-67; Coverage: 100%)
Gene names: rpl24e, rrnAC0104
Sequence domains: Ribosomal protein L24e
Structure domains: Ribosomal protein L24e
50S ribosomal protein L29 Chain: V
Molecule details ›
Chain: V
Length: 71 amino acids
Theoretical weight: 7.89 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10971 (Residues: 1-71; Coverage: 100%)
Gene names: rpl29, rrnAC1604
Sequence domains: Ribosomal L29 protein
Structure domains: Helix Hairpins
50S ribosomal protein L30 Chain: W
Molecule details ›
Chain: W
Length: 154 amino acids
Theoretical weight: 17.06 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14121 (Residues: 1-154; Coverage: 100%)
Gene names: rpl30, rrnAC1591
Sequence domains: Ribosomal protein L30p/L7e
Structure domains:
50S ribosomal protein L31e Chain: X
Molecule details ›
Chain: X
Length: 92 amino acids
Theoretical weight: 10.38 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P18138 (Residues: 1-92; Coverage: 100%)
Gene names: rpl31e, rrnAC3113
Sequence domains: Ribosomal protein L31e
Structure domains: Ribosomal Protein L31e; Chain: W;
50S ribosomal protein L32e Chain: Y
Molecule details ›
Chain: Y
Length: 240 amino acids
Theoretical weight: 26.33 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12736 (Residues: 1-240; Coverage: 100%)
Gene names: rpl32e, rrnAC1595
Sequence domains:
50S ribosomal protein L37Ae Chain: Z
Molecule details ›
Chain: Z
Length: 116 amino acids
Theoretical weight: 12.9 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60619 (Residues: 1-92; Coverage: 100%)
Gene names: rpl37ae, rrnAC1669
Sequence domains: Ribosomal L37ae protein family
Structure domains: N-terminal domain of TfIIb
50S ribosomal protein L37e Chain: 1
Molecule details ›
Chain: 1
Length: 57 amino acids
Theoretical weight: 6.33 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32410 (Residues: 1-57; Coverage: 100%)
Gene names: rpl37e, rrnAC0797.1
Sequence domains: Ribosomal protein L37e
Structure domains: N-terminal domain of TfIIb
50S ribosomal protein L39e Chain: 2
Molecule details ›
Chain: 2
Length: 50 amino acids
Theoretical weight: 6.13 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22452 (Residues: 1-50; Coverage: 100%)
Gene names: rpl39e, rrnAC3112
Sequence domains: Ribosomal L39 protein
Structure domains: Ribosomal protein L39e
50S ribosomal protein L44e Chain: 3
Molecule details ›
Chain: 3
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32411 (Residues: 1-92; Coverage: 100%)
Gene names: rpl44e, rrnAC3514
Sequence domains: Ribosomal protein L44
Structure domains: Nuclear Transport Factor 2; Chain: A,
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2923 nucleotides
Theoretical weight: 946.46 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
5S ribosomal RNA Chain: 9
Molecule details ›
Chain: 9
Length: 122 nucleotides
Theoretical weight: 39.3 KDa
Sequence domains: 5S ribosomal RNA
RNA (5'-R(*CP*CP*A)-3') Chain: 5
Molecule details ›
Chain: 5
Length: 3 nucleotides
Theoretical weight: 895 Da
RNA (5'-R(*CP*CP*(8AN))-3') Chain: 6
Molecule details ›
Chain: 6
Length: 3 nucleotides
Theoretical weight: 894 Da

Ligands and Environments

8 bound ligands:
Ligand MG 93 x MG
Ligand CL 22 x CL
Ligand SR 107 x SR
Ligand NA 75 x NA
Ligand CD 5 x CD
Ligand K 2 x K
Ligand PHE 1 x PHE
Ligand ACA 1 x ACA
6 modified residues:
Ligand 1MA 1 x 1MA
Ligand OMU 1 x OMU
Ligand OMG 1 x OMG
Ligand UR3 1 x UR3
Ligand PSU 1 x PSU
Ligand 8AN 1 x 8AN

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 211.316Å b: 297.905Å c: 573.138Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.194 0.245

Quick links

Citations

7 review citations

tRNA Modifications: Impact on Structure and Thermal Adaptation.
Lorenz et al. (2017)
6 more