4K1C

VCX1 Calcium/Proton Exchanger


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 10.1038/nature12233
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar calcium ion transporterA, B421Saccharomyces 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • 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

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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