7QBZ | pdb_00007qbz

Crystal structure Cadmium translocating P-type ATPase

• PDB DOI: https://doi.org/10.2210/pdb7QBZ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Sulfitobacter sp. NAS-14.1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2021-11-21 Released: 2022-03-23 
• Deposition Author(s): Groenberg, C., Hu, Q., Wang, K., Gourdon, P.
• Funding Organization(s): Lundbeckfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.255 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

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

• PubMed: 34951590 
• DOI: https://doi.org/10.7554/eLife.73124
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
Department of Chemistry, Umeå University, Umeå, Sweden.
Department of Sciences, University of Copenhagen, Copenhagen, Denmark.
Department of Laboratory Medicine, Lund University, Lund, Sweden.
Department of Chemistry and Biochemistry, The University of Texas, Dallas, United States.
Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
Department of Experimental Medical Science, Lund University, Lund, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.78 kDa 
• Atom Count: 4,701 
• Modeled Residue Count: 638 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadmium translocating P-type ATPase	A	682	Sulfitobacter sp. NAS-14.1	Mutation(s): 0  Gene Names: NAS141_02821 EC: 7.2.2.12 Membrane Entity: Yes
UniProt
Find proteins for A0A7W6H2S1 (Sulfitobacter undariae) Explore A0A7W6H2S1  Go to UniProtKB:  A0A7W6H2S1
Find proteins for A0ABY0T1R9 (Sulfitobacter litoralis) Explore A0ABY0T1R9  Go to UniProtKB:  A0ABY0T1R9
UniProt Groups	A0ABY0T1R9A0A7W6H2S1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ALF (Subject of Investigation/LOI)	B [auth A]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.255 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.642	α = 90
b = 93.665	β = 90
c = 128.258	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Groenberg, C., Hu, Q., Wang, K., Gourdon, P.

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Funding Organization	Location	Grant Number
Lundbeckfonden	Denmark	R133-A12689

Revision History  

• 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
• Version 1.3: 2026-09-02
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Advisory, Derived calculations, Structure summary