4FTG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5054 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


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.,Sect.D 69: 92-104

  • DOI: 10.1107/S0907444912043429

  • 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 locali ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A10
A, B
96Homo sapiensGene Names: S100A10 (ANX2LG, CAL1L, CLP11)
Find proteins for P60903 (Homo sapiens)
Go to Gene View: S100A10
Go to UniProtKB:  P60903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Annexin A2
C, D
17Homo sapiensGene Names: ANXA2 (ANX2, ANX2L4, CAL1H, LPC2D)
Find proteins for P07355 (Homo sapiens)
Go to Gene View: ANXA2
Go to UniProtKB:  P07355
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Neuroblast differentiation-associated protein AHNAK
E
22Homo sapiensGene Names: AHNAK (PM227)
Find proteins for Q09666 (Homo sapiens)
Go to Gene View: AHNAK
Go to UniProtKB:  Q09666
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B, E
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C, D, E
NON-POLYMERH2 N

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ACE
Query on ACE
C, D, E
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5054 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.072α = 90.00
b = 55.216β = 111.73
c = 63.140γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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