2ZBF

Calcium pump crystal structure with bound BeF3 and TG in the absence of calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump

Toyoshima, C.Norimatsu, Y.Iwasawa, S.Tsuda, T.Ogawa, H.

(2007) Proc.Natl.Acad.Sci.Usa 104: 19831-19836

  • DOI: 10.1073/pnas.0709978104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum is the best-studied member of the P-type or E1/E2 type ion transporting ATPases. It has been crystallized in seven different states that cover nearly the entire reaction cycle. Here we describe ...

    Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum is the best-studied member of the P-type or E1/E2 type ion transporting ATPases. It has been crystallized in seven different states that cover nearly the entire reaction cycle. Here we describe the structure of this ATPase complexed with phosphate analogs BeF(3)(-) and AlF(4)(-) in the absence of Ca(2+), which correspond to the E2P ground state and E2 approximately P transition state, respectively. The luminal gate is open with BeF(3)(-) and closed with AlF(4)(-). These and the E1 approximately P.ADP analog crystal structures show that a two-step rotation of the cytoplasmic A-domain opens and closes the luminal gate through the movements of the M1-M4 transmembrane helices. There are several conformational switches coupled to the rotation, and the one in the cytoplasmic part of M2 has critical importance. In the second step of rotation, positioning of one water molecule couples the hydrolysis of aspartylphosphate to closing of the gate.


    Related Citations: 
    • 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
    • Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
      Toyoshima, C.,Nomura, H.,Tsuda, T.
      (2004) Nature 432: 361
    • 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
    • Structural changes in the calcium pump accompanying the dissociation of calcium
      Toyoshima, C.,Nomura, H.
      (2002) Nature 418: 605
    • 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
    • Crystal structure of the calcium pump with a bound ATP analogue
      Toyoshima, C.,Mizutani, T.
      (2004) Nature 430: 529


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TG1
Query on TG1

Download SDF File 
Download CCD File 
A
OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER
THAPSIGARGIN
C34 H50 O12
IXFPJGBNCFXKPI-FSIHEZPISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TG1IC50: 0.2 nM (100) BINDINGDB
TG1Kd: 0.2 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 90.522α = 90.00
b = 136.473β = 90.00
c = 106.619γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance