2YFY | pdb_00002yfy

SERCA in the HnE2 State Complexed With Debutanoyl Thapsigargin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.278 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2YFY

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Mutual Adaptation of a Membrane Protein and its Lipid Bilayer During Conformational Changes.

Sonntag, Y.Musgaard, M.Olesen, C.Schiott, B.Moller, J.V.Nissen, P.Thogersen, L.

(2011) Nat Commun 2: 304

  • DOI: https://doi.org/10.1038/ncomms1307
  • Primary Citation Related Structures: 
    2YFY

  • PubMed Abstract: 

    The structural elucidation of membrane proteins continues to gather pace, but we know little about their molecular interactions with the lipid environment or how they interact with the surrounding bilayer. Here, with the aid of low-resolution X-ray crystallography, we present direct structural information on membrane interfaces as delineated by lipid phosphate groups surrounding the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) in its phosphorylated and dephosphorylated Ca(2+)-free forms. The protein-lipid interactions are further analysed using molecular dynamics simulations. We find that SERCA adapts to membranes of different hydrophobic thicknesses by inducing local deformations in the lipid bilayers and by undergoing small rearrangements of the amino-acid side chains and helix tilts. These mutually adaptive interactions allow smooth transitions through large conformational changes associated with the transport cycle of SERCA, a strategy that may be of general nature for many membrane proteins.


  • Organizational Affiliation
    • Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, DK-8000 Aarhus C, Denmark.

Macromolecule Content 

  • Total Structure Weight: 110.25 kDa 
  • Atom Count: 7,714 
  • Modeled Residue Count: 994 
  • Deposited Residue Count: 994 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1994Oryctolagus cuniculusMutation(s): 0 
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.278 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.36α = 90
b = 71.36β = 90
c = 587.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary