Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 220506.66 
• Atom Count: 15434 
• Residue Count: 1988 
• Unique protein chains: 1

1IWO

Crystal structure of the SR Ca2+-ATPase in the absence of Ca2+

• DOI: 10.2210/pdb1IWO/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Oryctolagus cuniculus


• Deposited: 2002-05-26 Released: 2002-08-14 
• Deposition Author(s): Toyoshima, C., Nomura, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.268 
• R-Value Work: 0.237 

Literature

Structural changes in the calcium pump accompanying the dissociation of calcium

Toyoshima, C., Nomura, H.

(2002) Nature 418: 605-611

• PubMed: 12167852 
• DOI: 10.1038/nature00944
• Also Cited By: 2ZBG, 2ZBF, 2ZBE, 2ZBD, 2Z9R, 2EAU, 2EAT, 2EAS, 2EAR, 2DQS


• PubMed Abstract: 
  

In skeletal muscle, calcium ions are transported (pumped) against a concentration gradient from the cytoplasm into the sarcoplasmic reticulum, an intracellular organelle. This causes muscle cells to relax after cytosolic calcium increases during excitation. The Ca(2+) ATPase that carries out this pumping is a representative P-type ion-transporting ATPase. Here we describe the structure of this ion pump at 3.1 A resolution in a Ca(2+)-free (E2) state, and compare it with that determined previously for the Ca(2+)-bound (E1Ca(2+)) state. The structure of the enzyme stabilized by thapsigargin, a potent inhibitor, shows large conformation differences from that in E1Ca(2+). Three cytoplasmic domains gather to form a single headpiece, and six of the ten transmembrane helices exhibit large-scale rearrangements. These rearrangements ensure the release of calcium ions into the lumen of sarcoplasmic reticulum and, on the cytoplasmic side, create a pathway for entry of new calcium ions.

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Related Citations: 

• The crystal and molecular structure of the sesquiterpenoid silerin (trilobolide)
  Kutschabsky, L.,Kretschmer, R.-G.,Ripperger, H.
  (1986) Cryst.Res.Technol. 21: 627
• 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
• Sesquiterpenoids from Thapsia species and medicinal chemistry of the thapsigargins
  Christensen, S.B.,Andersen, A.,Smitt, U.W.
  (1997) Fortschr.Chem.Org.Naturst. 71: 129




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Organizational Affiliation: 

Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A, B	994	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: ATP2A1 EC: 7.2.2.10
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  P-type ATPase	Protein:  Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium
Find proteins for P04191 (Oryctolagus cuniculus) Go to Gene View: ATP2A1 Go to UniProtKB:  P04191

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TG1	A, B	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TG1	Kd: 0.2 nM (100) BINDINGDB
TG1	IC50: 0.2 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.268 
• R-Value Work: 0.237 
• Space Group: P 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 71.739	α = 90.00
b = 71.739	β = 90.00
c = 590.300	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
X-PLOR	phasing
SCALEPACK	data scaling
X-PLOR	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-26 
• Released Date: 2002-08-14 
• Deposition Author(s): Toyoshima, C., Nomura, H.

Revision History 

• Version 1.0: 2002-08-14
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance