4FTG

The crystal structure of an AHNAK peptide in complex with the S100A10/AnxA2 heterotetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.185 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a C-terminal AHNAK peptide in a 1:2:2 complex with S100A10 and an acetylated N-terminal peptide of annexin A2.

Ozorowski, G.Milton, S.Luecke, H.

(2013) Acta Crystallogr D Biol Crystallogr 69: 92-104

  • DOI: https://doi.org/10.1107/S0907444912043429
  • Primary Citation of Related Structures:  
    4FTG

  • PubMed Abstract: 

    AHNAK, a large 629 kDa protein, has been implicated in membrane repair, and the annexin A2-S100A10 heterotetramer [(p11)(2)(AnxA2)(2))] has high affinity for several regions of its 1002-amino-acid C-terminal domain. (p11)(2)(AnxA2)(2) is often localized near the plasma membrane, and this C2-symmetric platform is proposed to be involved in the bridging of membrane vesicles and trafficking of proteins to the plasma membrane. All three proteins co-localize at the intracellular face of the plasma membrane in a Ca(2+)-dependent manner. The binding of AHNAK to (p11)(2)(AnxA2)(2) has been studied previously, and a minimal binding motif has been mapped to a 20-amino-acid peptide corresponding to residues 5654-5673 of the AHNAK C-terminal domain. Here, the 2.5 Å resolution crystal structure of this 20-amino-acid peptide of AHNAK bound to the AnxA2-S100A10 heterotetramer (1:2:2 symmetry) is presented, which confirms the asymmetric arrangement first described by Rezvanpour and coworkers and explains why the binding motif has high affinity for (p11)(2)(AnxA2)(2). Binding of AHNAK to the surface of (p11)(2)(AnxA2)(2) is governed by several hydrophobic interactions between side chains of AHNAK and pockets on S100A10. The pockets are large enough to accommodate a variety of hydrophobic side chains, allowing the consensus sequence to be more general. Additionally, the various hydrogen bonds formed between the AHNAK peptide and (p11)(2)(AnxA2)(2) most often involve backbone atoms of AHNAK; as a result, the side chains, particularly those that point away from S100A10/AnxA2 towards the solvent, are largely interchangeable. While the structure-based consensus sequence allows interactions with various stretches of the AHNAK C-terminal domain, comparison with other S100 structures reveals that the sequence has been optimized for binding to S100A10. This model adds new insight to the understanding of the specific interactions that occur in this membrane-repair scaffold.


  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, 92697-3900, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A10
A, B
96Homo sapiensMutation(s): 0 
Gene Names: ANX2LGCAL1LCLP11S100A10
UniProt & NIH Common Fund Data Resources
Find proteins for P60903 (Homo sapiens)
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Go to UniProtKB:  P60903
PHAROS:  P60903
GTEx:  ENSG00000197747 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60903
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Annexin A2
C, D
17Homo sapiensMutation(s): 3 
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Find proteins for P07355 (Homo sapiens)
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Go to UniProtKB:  P07355
PHAROS:  P07355
GTEx:  ENSG00000182718 
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UniProt GroupP07355
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Neuroblast differentiation-associated protein AHNAK22Homo sapiensMutation(s): 2 
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Find proteins for Q09666 (Homo sapiens)
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Go to UniProtKB:  Q09666
PHAROS:  Q09666
GTEx:  ENSG00000124942 
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UniProt GroupQ09666
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.072α = 90
b = 55.216β = 111.73
c = 63.14γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-02-20
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description