3J7T

Calcium atpase structure with two bound calcium ions determined by electron crystallography of thin 3D crystals


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Electron crystallography of ultrathin 3D protein crystals: atomic model with charges

Yonekura, K.Kato, K.Ogasawara, M.Tomita, M.Toyoshima, C.

(2015) Proc.Natl.Acad.Sci.USA 112: 3368-3373

  • DOI: 10.1073/pnas.1500724112
  • Primary Citation of Related Structures:  
  • Also Cited By: 5GKN

  • PubMed Abstract: 
  • Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, a ...

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.


    Organizational Affiliation

    Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
A
994Oryctolagus cuniculusMutation(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. E1 state with bound calcium
Find proteins for P04191 (Oryctolagus cuniculus)
Go to Gene View: ATP2A1
Go to UniProtKB:  P04191
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references