2ZBD

Crystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues

Toyoshima, C.Nomura, H.Tsuda, T.

(2004) Nature 432: 361-368

  • DOI: 10.1038/nature02981
  • Primary Citation of Related Structures:  
  • Also Cited By: 2ZBG, 2ZBF, 2ZBE, 2EAU, 2EAT, 2EAS, 2EAR, 2DQS

  • PubMed Abstract: 
  • P-type ion transporting ATPases are ATP-powered ion pumps that establish ion concentration gradients across biological membranes. Transfer of bound cations to the lumenal or extracellular side occurs while the ATPase is phosphorylated. Here we report ...

    P-type ion transporting ATPases are ATP-powered ion pumps that establish ion concentration gradients across biological membranes. Transfer of bound cations to the lumenal or extracellular side occurs while the ATPase is phosphorylated. Here we report at 2.3 A resolution the structure of the calcium-ATPase of skeletal muscle sarcoplasmic reticulum, a representative P-type ATPase that is crystallized in the absence of Ca2+ but in the presence of magnesium fluoride, a stable phosphate analogue. This and other crystal structures determined previously provide atomic models for all four principal states in the reaction cycle. These structures show that the three cytoplasmic domains rearrange to move six out of ten transmembrane helices, thereby changing the affinity of the Ca2+-binding sites and the gating of the ion pathway. Release of ADP triggers the opening of the lumenal gate and release of phosphate its closure, effected mainly through movement of the A-domain, the actuator of transmembrane gates.


    Related Citations: 
    • Crystal structure of the calcium pump with a bound ATP analogue
      Toyoshima, C.,Mizutani, T.
      (2004) Nature 430: 529
    • Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
      Toyoshima, C.,Nakasako, M.,Nomura, H.,Ogawa, H.
      (2000) Nature 405: 647
    • Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors
      Takahashi, M.,Kondou, Y.,Toyoshima, C.
      (2007) Proc.Natl.Acad.Sci.Usa 104: 5800
    • Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)
      Obara, K.,Miyashita, N.,Xu, C.,Toyoshima, I.,Sugita, Y.,Inesi, G.,Toyoshima, C.
      (2005) Proc.Natl.Acad.Sci.Usa 102: 14489
    • Structural changes in the calcium pump accompanying the dissociation of calcium
      Toyoshima, C.,Nomura, H.
      (2002) Nature 418: 605


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. ct@iam.u-tokyo.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
A
995Oryctolagus cuniculusMutation(s): 0 
Gene Names: ATP2A1
EC: 3.6.3.8
Find proteins for P04191 (Oryctolagus cuniculus)
Go to Gene View: ATP2A1
Go to UniProtKB:  P04191
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PC1
Query on PC1

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Download CCD File 
A
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ALF
Query on ALF

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Download CCD File 
A
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.900α = 90.00
b = 75.100β = 109.30
c = 152.100γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance