2VJ0

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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This is version 1.2 of the entry. See complete history


Literature

Solitary and Repetitive Binding Motifs for the Ap2 Complex {Alpha}-Appendage in Amphiphysin and Other Accessory Proteins.

Olesen, L.E.Ford, M.G.J.Schmid, E.M.Vallis, Y.Madan Babu, M.Li, P.H.Mills, I.G.Mcmahon, H.T.Praefcke, G.J.K.

(2008) J Biol Chem 283: 5099

  • DOI: 10.1074/jbc.M708621200
  • Primary Citation of Related Structures:  
    2VJ0

  • PubMed Abstract: 
  • Adaptor protein (AP) complexes bind to transmembrane proteins destined for internalization and to membrane lipids, so linking cargo to the accessory internalization machinery. This machinery interacts with the appendage domains of APs, which have platform and beta-sandwich subdomains, forming the binding surfaces for interacting proteins ...

    Adaptor protein (AP) complexes bind to transmembrane proteins destined for internalization and to membrane lipids, so linking cargo to the accessory internalization machinery. This machinery interacts with the appendage domains of APs, which have platform and beta-sandwich subdomains, forming the binding surfaces for interacting proteins. Proteins that interact with the subdomains do so via short motifs, usually found in regions of low structural complexity of the interacting proteins. So far, up to four motifs have been identified that bind to and partially compete for at least two sites on each of the appendage domains of the AP2 complex. Motifs in individual accessory proteins, their sequential arrangement into motif domains, and partial competition for binding sites on the appendage domains coordinate the formation of endocytic complexes in a temporal and spatial manner. In this work, we examine the dominant interaction sequence in amphiphysin, a synapse-enriched accessory protein, which generates membrane curvature and recruits the scission protein dynamin to the necks of coated pits, for the platform subdomain of the alpha-appendage. The motif domain of amphiphysin1 contains one copy of each of a DX(F/W) and FXDXF motif. We find that the FXDXF motif is the main determinant for the high affinity interaction with the alpha-adaptin appendage. We describe the optimal sequence of the FXDXF motif using thermodynamic and structural data and show how sequence variation controls the affinities of these motifs for the alpha-appendage.


    Organizational Affiliation

    Laboratory of Molecular Biology, Medical Research Council, Neurobiology Division, Hills Road, Cambridge CB2 2QH, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AP-2 COMPLEX SUBUNIT ALPHA-2A250Mus musculusMutation(s): 0 
Gene Names: Ap2a2Adtab
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus)
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Go to UniProtKB:  P17427
IMPC:  MGI:101920
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SYNAPTOJANIN-1B [auth P]12Homo sapiensMutation(s): 0 
Gene Names: SYNJ1KIAA0910
EC: 3.1.3.36
UniProt & NIH Common Fund Data Resources
Find proteins for O43426 (Homo sapiens)
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Go to UniProtKB:  O43426
PHAROS:  O43426
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AMPHIPHYSINC [auth Q]7Rattus norvegicusMutation(s): 0 
Gene Names: AmphAmph1
Membrane Entity: Yes 
UniProt
Find proteins for O08838 (Rattus norvegicus)
Explore O08838 
Go to UniProtKB:  O08838
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTD (Subject of Investigation/LOI)
Query on DTD

Download Ideal Coordinates CCD File 
E [auth A]DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
 Ligand Interaction
BEN
Query on BEN

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D [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.508α = 90
b = 66.98β = 94.92
c = 39.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance