8Q76

Copper-transporting ATPase HMA4 in E2P state with BeF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Diverse roles of the metal binding domains and transport mechanism of copper transporting P-type ATPases.

Guo, Z.Oradd, F.Bagenholm, V.Gronberg, C.Ma, J.F.Ott, P.Wang, Y.Andersson, M.Pedersen, P.A.Wang, K.Gourdon, P.

(2024) Nat Commun 15: 2690-2690

  • DOI: https://doi.org/10.1038/s41467-024-47001-4
  • Primary Citation of Related Structures:  
    8Q73, 8Q74, 8Q75, 8Q76

  • PubMed Abstract: 

    Copper transporting P-type (P 1B-1 -) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P 1B-1 -ATPases remains poorly understood. In particular, the role of the intrinsic metal binding domains (MBDs) is enigmatic. Here, four cryo-EM structures and molecular dynamics simulations of a P 1B-1 -ATPase are combined to reveal that in many eukaryotes the MBD immediately prior to the ATPase core, MBD -1 , serves a structural role, remodeling the ion-uptake region. In contrast, the MBD prior to MBD -1 , MBD -2 , likely assists in copper delivery to the ATPase core. Invariant Tyr, Asn and Ser residues in the transmembrane domain assist in positioning sulfur-providing copper-binding amino acids, allowing for copper uptake, binding and release. As such, our findings unify previously conflicting data on the transport and regulation of P 1B-1 -ATPases. The results are critical for a fundamental understanding of cellular copper homeostasis and for comprehension of the molecular bases of P 1B-1 -disorders and ongoing clinical trials.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-transporting ATPase HMA4978Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: HMA4
UniProt
Find proteins for Q6H7M3 (Oryza sativa subsp. japonica)
Explore Q6H7M3 
Go to UniProtKB:  Q6H7M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6H7M3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR133-A12689
LundbeckfondenDenmarkR324-2019-1855

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release