6HEF

Room temperature structure of the (SR)Ca2+-ATPase Ca2-E1-CaAMPPCP form

• PDB DOI: https://doi.org/10.2210/pdb6HEF/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-08-20 Released: 2018-08-29 
• Deposition Author(s): Hjorth-Jensen, S., Sorensen, T.L.M., Oksanen, E., Andersen, J.L., Olesen, C., Moller, J.V., Nissen, P.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.54 Å
• R-Value Free: 0.257 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Literature

Membrane-protein crystals for neutron diffraction.

Sorensen, T.L.M., Hjorth-Jensen, S.J., Oksanen, E., Andersen, J.L., Olesen, C., Moller, J.V., Nissen, P.

(2018) Acta Crystallogr D Struct Biol 74: 1208-1218

• PubMed: 30605135 
• DOI: https://doi.org/10.1107/S2059798318012561
• Primary Citation of Related Structures:  
  6HEF


• PubMed Abstract: 
  

  Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1. The challenges encountered at the various steps in the process from crystal nucleation and growth to crystal mounting are explored, and it is demonstrated that NMX-compatible membrane-protein crystals can indeed be obtained.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.05 kDa 
• Atom Count: 7,760 
• Modelled Residue Count: 994 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	994	Oryctolagus cuniculus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191  Go to UniProtKB:  P04191

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	G [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
ACP	B [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.54 Å
• R-Value Free: 0.257 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.84	α = 90
b = 77.77	β = 109.28
c = 152.22	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Hjorth-Jensen, S., Sorensen, T.L.M., Oksanen, E., Andersen, J.L., Olesen, C., Moller, J.V., Nissen, P.

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Funding Organization	Location	Grant Number
European Commission	Denmark	722687

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description