Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 220.51 kDa 
• 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
• Mutation(s): No 


• 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: 3.10 Å
• R-Value Free: 0.268 
• R-Value Work: 0.237 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  1IWO


• 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: 

• 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

• The crystal and molecular structure of the sesquiterpenoid silerin (trilobolide)
  Kutschabsky, L., Kretschmer, R.-G., Ripperger, H.
  (1986) Cryst Res Technol 21: 627

• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A, B	994	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: ATP2A1 EC: 7.2.2.10
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  P-type ATPase	Protein:  Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state without bound calcium
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191  Go to UniProtKB:  P04191

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER C34 H50 O12 IXFPJGBNCFXKPI-FSIHEZPISA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TG1	IC50:  0.20000000298023224   nM  BindingDB
TG1	Kd:  0.20000000298023224   nM  BindingDB
TG1	Ki:  0.10000000149011612   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.268 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.739	α = 90
b = 71.739	β = 90
c = 590.3	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance