7R0G

STRUCTURAL BASIS OF ION UPTAKE IN COPPER-TRANSPORTING P1B-TYPE ATPASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.01 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.267 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of ion uptake in copper-transporting P 1B -type ATPases.

Salustros, N.Gronberg, C.Abeyrathna, N.S.Lyu, P.Oradd, F.Wang, K.Andersson, M.Meloni, G.Gourdon, P.

(2022) Nat Commun 13: 5121-5121

  • DOI: https://doi.org/10.1038/s41467-022-32751-w
  • Primary Citation of Related Structures:  
    7R0G, 7R0H, 7R0I

  • PubMed Abstract: 

    Copper is essential for living cells, yet toxic at elevated concentrations. Class 1B P-type (P 1B -) ATPases are present in all kingdoms of life, facilitating cellular export of transition metals including copper. P-type ATPases follow an alternating access mechanism, with inward-facing E1 and outward-facing E2 conformations. Nevertheless, no structural information on E1 states is available for P 1B -ATPases, hampering mechanistic understanding. Here, we present structures that reach 2.7 Å resolution of a copper-specific P 1B -ATPase in an E1 conformation, with complementing data and analyses. Our efforts reveal a domain arrangement that generates space for interaction with ion donating chaperones, and suggest a direct Cu + transfer to the transmembrane core. A methionine serves a key role by assisting the release of the chaperone-bound ion and forming a cargo entry site together with the cysteines of the CPC signature motif. Collectively, the findings provide insights into P 1B -mediated transport, likely applicable also to human P 1B -members.


  • Organizational Affiliation

    Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative copper-exporting P-type ATPase A
A, B
658Archaeoglobus fulgidusMutation(s): 0 
Gene Names: XD40_1059XD48_1194
EC: 7.2.2.8
Membrane Entity: Yes 
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: 4.01 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.194α = 90
b = 226.056β = 134.062
c = 111.106γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description