4K1C | pdb_00004k1c

VCX1 Calcium/Proton Exchanger


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.225 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4K1C

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural basis for alternating access of a eukaryotic calcium/proton exchanger.

Waight, A.B.Pedersen, B.P.Schlessinger, A.Bonomi, M.Chau, B.H.Roe-Zurz, Z.Risenmay, A.J.Sali, A.Stroud, R.M.

(2013) Nature 499: 107-110

  • DOI: https://doi.org/10.1038/nature12233
  • Primary Citation Related Structures: 
    4K1C

  • PubMed Abstract: 

    Eukaryotic Ca(2+) regulation involves sequestration into intracellular organelles, and expeditious Ca(2+) release into the cytosol is a hallmark of key signalling transduction pathways. Bulk removal of Ca(2+) after such signalling events is accomplished by members of the Ca(2+):cation (CaCA) superfamily. The CaCA superfamily includes the Na(+)/Ca(2+) (NCX) and Ca(2+)/H(+) (CAX) antiporters, and in mammals the NCX and related proteins constitute families SLC8 and SLC24, and are responsible for the re-establishment of Ca(2+) resting potential in muscle cells, neuronal signalling and Ca(2+) reabsorption in the kidney. The CAX family members maintain cytosolic Ca(2+) homeostasis in plants and fungi during steep rises in intracellular Ca(2+) due to environmental changes, or following signal transduction caused by events such as hyperosmotic shock, hormone response and response to mating pheromones. The cytosol-facing conformations within the CaCA superfamily are unknown, and the transport mechanism remains speculative. Here we determine a crystal structure of the Saccharomyces cerevisiae vacuolar Ca(2+)/H(+) exchanger (Vcx1) at 2.3 Å resolution in a cytosol-facing, substrate-bound conformation. Vcx1 is the first structure, to our knowledge, within the CAX family, and it describes the key cytosol-facing conformation of the CaCA superfamily, providing the structural basis for a novel alternating access mechanism by which the CaCA superfamily performs high-throughput Ca(2+) transport across membranes.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA.

Macromolecule Content 

  • Total Structure Weight: 95.31 kDa 
  • Atom Count: 5,933 
  • Modeled Residue Count: 745 
  • Deposited Residue Count: 842 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar calcium ion transporter
A, B
421Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VCX1HUM1MNR1YDL128W
Membrane Entity: Yes 
UniProt
Find proteins for Q99385 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99385 
Go to UniProtKB:  Q99385
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99385
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC

Query on OLC



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
X [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
DA [auth B]
EA [auth B]
N [auth A]
O [auth A]
P [auth A]
DA [auth B],
EA [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
MN

Query on MN



Download:Ideal Coordinates CCD File
CA [auth B],
M [auth A],
W [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
H [auth A]
I [auth A]
J [auth A]
AA [auth B],
BA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Y [auth B],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.11α = 90
b = 130.11β = 90
c = 156.75γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations