4BBJ | pdb_00004bbj

Copper-transporting PIB-ATPase in complex with beryllium fluoride representing the E2P state

• PDB DOI: https://doi.org/10.2210/pdb4BBJ/pdb

• Classification: HYDROLASE
• Organism(s): Legionella pneumophila subsp. pneumophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2012-09-25 Released: 2013-12-11 
• Deposition Author(s): Mattle, D., Gourdon, P., Nissen, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Copper-Transporting P-Type Atpases Use a Unique Ion-Release Pathway

Andersson, M., Mattle, D., Sitsel, O., Klymchuk, T., Nielsen, A., Moller, L.B., White, S.H., Nissen, P., Gourdon, P.

(2014) Nat Struct Mol Biol 21: 43

• PubMed: 24317491 
• DOI: https://doi.org/10.1038/nsmb.2721
• Primary Citation Related Structures: 
  4BBJ


• PubMed Abstract: 
  

  Heavy metals in cells are typically regulated by PIB-type ATPases. The first structure of the class, a Cu(+)-ATPase from Legionella pneumophila (LpCopA), outlined a copper transport pathway across the membrane, which was inferred to be occluded. Here we show by molecular dynamics simulations that extracellular water solvated the transmembrane (TM) domain, results indicative of a Cu(+)-release pathway. Furthermore, a new LpCopA crystal structure determined at 2.8-Å resolution, trapped in the preceding E2P state, delineated the same passage, and site-directed-mutagenesis activity assays support a functional role for the conduit. The structural similarities between the TM domains of the two conformations suggest that Cu(+)-ATPases couple dephosphorylation and ion extrusion differently than do the well-characterized PII-type ATPases. The ion pathway explains why certain Menkes' and Wilson's disease mutations impair protein function and points to a site for inhibitors targeting pathogens.

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Organizational Affiliation: 
• 1] Department of Physiology and Biophysics, University of California at Irvine, Irvine, California, USA. [2] [3].
1] Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. [2] [3].
Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark.
Department of Physiology and Biophysics, University of California at Irvine, Irvine, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.81 kDa 
• Atom Count: 5,096 
• Modeled Residue Count: 664 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER EFFLUX ATPASE	A	736	Legionella pneumophila subsp. pneumophila	Mutation(s): 0  EC: 3.6.3 (PDB Primary Data), 7.2.2.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5ZWR1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWR1  Go to UniProtKB:  Q5ZWR1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CE1	D [auth A]	O-DODECANYL OCTAETHYLENE GLYCOL C28 H58 O9 YYELLDKEOUKVIQ-UHFFFAOYSA-N
PC	E [auth A]	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BFD	A	L-PEPTIDE LINKING	C4 H6 Be F3 N O4		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.01	α = 90
b = 71.37	β = 100.01
c = 72.43	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Mattle, D., Gourdon, P., Nissen, P.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary