2EAT

Crystal structure of the SR CA2+-ATPASE with bound CPA and TG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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 U S A 104: 5800-5805

  • DOI: 10.1073/pnas.0700979104
  • Primary Citation of Related Structures:  
    2EAR, 2EAT, 2EAU, 4YCL

  • PubMed Abstract: 
  • Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum is an ATP-driven Ca(2+) pump consisting of three cytoplasmic domains and 10 transmembrane helices. In the absence of Ca(2+), the three cytoplasmic domains gather to form a compact headpiece, but the ATPase is unstable without an inhibitor ...

    Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum is an ATP-driven Ca(2+) pump consisting of three cytoplasmic domains and 10 transmembrane helices. In the absence of Ca(2+), the three cytoplasmic domains gather to form a compact headpiece, but the ATPase is unstable without an inhibitor. Here we describe the crystal structures of Ca(2+)-ATPase in the absence of Ca(2+) stabilized with cyclopiazonic acid alone and in combination with other inhibitors. Cyclopiazonic acid is located in the transmembrane region of the protein near the cytoplasmic surface. The binding site partially overlaps with that of 2,5-di-tert-butyl-1,4-dihydroxybenzene but is separate from that of thapsigargin. The overall structure is significantly different from that stabilized with thapsigargin: The cytoplasmic headpiece is more upright, and the transmembrane helices M1-M4 are rearranged. Cyclopiazonic acid primarily alters the position of the M1' helix and thereby M2 and M4 and then M5. Because M5 is integrated into the phosphorylation domain, the whole cytoplasmic headpiece moves. These structural changes show how an event in the transmembrane domain can be transmitted to the cytoplasmic domain despite flexible links between them. They also reveal that Ca(2+)-ATPase has considerable plasticity even when fixed by a transmembrane inhibitor, presumably to accommodate thermal fluctuations.


    Related Citations: 
    • 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
    • Crystal structure of the calcium pump with a bound ATP analogue
      Toyoshima, C., Mizutani, T.
      (2004) Nature 430: 529
    • Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
      Toyoshima, C., Nomura, H., Tsuda, T.
      (2004) Nature 432: 361
    • 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 U S A 102: 14489

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1A995Oryctolagus cuniculusMutation(s): 0 
Gene Names: ATP2A1
EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P04191 (Oryctolagus cuniculus)
Explore P04191 
Go to UniProtKB:  P04191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04191
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TG1
Query on TG1

Download Ideal Coordinates CCD File 
B [auth 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)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER
C34 H50 O12
IXFPJGBNCFXKPI-FSIHEZPISA-N
 Ligand Interaction
CZA
Query on CZA

Download Ideal Coordinates CCD File 
C [auth A](6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE
C20 H20 N2 O3
RLOAZVAJNNPPDI-DQYPLSBCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TG1 BindingDB:  2EAT Ki: 0.1 (nM) from 1 assay(s)
Kd: 0.2 (nM) from 1 assay(s)
IC50: min: 0.2, max: 3.9 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.899α = 90
b = 95.645β = 95.24
c = 155.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-04-23
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance