3A1D | pdb_00003a1d

Crystal structure of the P- and N-domains of CopA, a copper-transporting P-type ATPase, bound with ADP-Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Nucleotide recognition by CopA, a Cu+-transporting P-type ATPase.

Tsuda, T.Toyoshima, C.

(2009) EMBO J 28: 1782-1791

  • DOI: https://doi.org/10.1038/emboj.2009.143
  • Primary Citation Related Structures: 
    3A1C, 3A1D, 3A1E

  • PubMed Abstract: 

    Heavy metal pumps constitute a large subgroup in P-type ion-transporting ATPases. One of the outstanding features is that the nucleotide binding N-domain lacks residues critical for ATP binding in other well-studied P-type ATPases. Instead, they possess an HP-motif and a Gly-rich sequence in the N-domain, and their mutations impair ATP binding. Here, we describe 1.85 A resolution crystal structures of the P- and N-domains of CopA, an archaeal Cu(+)-transporting ATPase, with bound nucleotides. These crystal structures show that CopA recognises the adenine ring completely differently from other P-type ATPases. The crystal structure of the His462Gln mutant, in the HP-motif, a disease-causing mutation in human Cu(+)-ATPases, shows that the Gln side chain mimics the imidazole ring, but only partially, explaining the reduction in ATPase activity. These crystal structures lead us to propose a role of the His and a mechanism for removing Mg(2+) from ATP before phosphoryl transfer.


  • Organizational Affiliation
    • Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 62.47 kDa 
  • Atom Count: 4,644 
  • Modeled Residue Count: 540 
  • Deposited Residue Count: 574 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable copper-exporting P-type ATPase A
A, B
287Archaeoglobus fulgidusMutation(s): 0 
Gene Names: copApacSAF_0473
EC: 3.6.3 (PDB Primary Data), 7.2.2.8 (UniProt)
UniProt
Find proteins for O29777 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29777 
Go to UniProtKB:  O29777
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29777
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.956α = 90
b = 89.956β = 90
c = 190.375γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description