7QBZ

Crystal structure Cadmium translocating P-type ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and ion-release mechanism of P IB-4 -type ATPases.

Gronberg, C.Hu, Q.Mahato, D.R.Longhin, E.Salustros, N.Duelli, A.Lyu, P.Bagenholm, V.Eriksson, J.Rao, K.U.Henderson, D.I.Meloni, G.Andersson, M.Croll, T.Godaly, G.Wang, K.Gourdon, P.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.73124
  • Primary Citation of Related Structures:  
    7QBZ, 7QC0

  • PubMed Abstract: 

    Transition metals, such as zinc, are essential micronutrients in all organisms, but also highly toxic in excessive amounts. Heavy-metal transporting P-type (P IB ) ATPases are crucial for homeostasis, conferring cellular detoxification and redistribution through transport of these ions across cellular membranes. No structural information is available for the P IB-4 -ATPases, the subclass with the broadest cargo scope, and hence even their topology remains elusive. Here, we present structures and complementary functional analyses of an archetypal P IB-4 -ATPase, sCoaT from Sulfitobacter sp. NAS14-1. The data disclose the architecture, devoid of classical so-called heavy-metal-binding domains (HMBDs), and provide fundamentally new insights into the mechanism and diversity of heavy-metal transporters. We reveal several novel P-type ATPase features, including a dual role in heavy-metal release and as an internal counter ion of an invariant histidine. We also establish that the turnover of P IB -ATPases is potassium independent, contrasting to many other P-type ATPases. Combined with new inhibitory compounds, our results open up for efforts in for example drug discovery, since P IB-4 -ATPases function as virulence factors in many pathogens.


  • Organizational Affiliation

    Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cadmium translocating P-type ATPase682Sulfitobacter sp. NAS-14.1Mutation(s): 0 
Gene Names: NAS141_02821
Membrane Entity: Yes 
UniProt
Find proteins for A3T2G5 (Sulfitobacter sp. (strain NAS-14.1))
Explore A3T2G5 
Go to UniProtKB:  A3T2G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3T2G5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.642α = 90
b = 93.665β = 90
c = 128.258γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR133-A12689

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description