6K25

Crystal structure of Ca-unbound human Annexin A5 in low salt condition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

High-resolution structures of annexin A5 in a two-dimensional array.

Hong, S.Na, S.Kim, O.H.Jeong, S.Oh, B.C.Ha, N.C.

(2020) J Struct Biol 209: 107401-107401

  • DOI: https://doi.org/10.1016/j.jsb.2019.10.003
  • Primary Citation of Related Structures:  
    6K22, 6K25

  • PubMed Abstract: 

    Annexins are soluble cytosolic proteins that bind to cell membranes. Annexin A5 self-assembles into a two-dimensional (2D) array and prevents cell rupture by attaching to damaged membranes. However, this process is not fully understood at the molecular level. In this study, we determined the crystal structures of annexin A5 with and without calcium (Ca 2+ ) and confirmed the Ca 2+ -dependent outward motion of a tryptophan residue. Strikingly, the two structures exhibited the same crystal packing and 2D arrangement into a p3 lattice, which agrees well with the results of low-resolution structural imaging. High-resolution structures indicated that a three-fold interaction near the tryptophan residue is important for mediating the formation of the p3 lattice. A hypothesis on the promotion of p3 lattice formation by phosphatidyl serine (PS) is also suggested. This study provides molecular insight into how annexins modulate the physical properties of cell membranes as a function of Ca 2+ concentration and the phospholipid composition of the membrane.


  • Organizational Affiliation

    Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Annexin A5331Homo sapiensMutation(s): 0 
Gene Names: ANXA5ANX5
UniProt & NIH Common Fund Data Resources
Find proteins for P08758 (Homo sapiens)
Explore P08758 
Go to UniProtKB:  P08758
PHAROS:  P08758
GTEx:  ENSG00000164111 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08758
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.512α = 90
b = 94.512β = 90
c = 136.701γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description