1W80

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Evolving Nature of the Ap2 Alpha-Appendage Hub During Clathrin-Coated Vesicle Endocytosis.

Praefcke, G.J.K., Ford, M.G.J., Schmid, E.M., Olesen, L.E., Gallop, J.L., Peak-Chew, S.-Y., Vallis, Y., Babu, M.M., Mills, I.G., Mcmahon, H.T.

(2004) Embo J. 23: 4371

  • DOI: 10.1038/sj.emboj.7600445

  • PubMed Abstract: 

    • Clathrin-mediated endocytosis involves the assembly of a network of proteins that select cargo, modify membrane shape and drive invagination, vesicle scission and uncoating. This network is initially assembled around adaptor protein (AP) appendage do ...

    Clathrin-mediated endocytosis involves the assembly of a network of proteins that select cargo, modify membrane shape and drive invagination, vesicle scission and uncoating. This network is initially assembled around adaptor protein (AP) appendage domains, which are protein interaction hubs. Using crystallography, we show that FxDxF and WVxF peptide motifs from synaptojanin bind to distinct subdomains on alpha-appendages, called 'top' and 'side' sites. Appendages use both these sites to interact with their binding partners in vitro and in vivo. Occupation of both sites simultaneously results in high-affinity reversible interactions with lone appendages (e.g. eps15 and epsin1). Proteins with multiple copies of only one type of motif bind multiple appendages and so will aid adaptor clustering. These clustered alpha(appendage)-hubs have altered properties where they can sample many different binding partners, which in turn can interact with each other and indirectly with clathrin. In the final coated vesicle, most appendage binding partners are absent and thus the functional status of the appendage domain as an interaction hub is temporal and transitory giving directionality to vesicle assembly.

    Organizational Affiliation: 

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT
A
250Mus musculusMutation(s): 0 
Gene Names: Ap2a2 (Adtab)
Find proteins for P17427 (Mus musculus)
Go to UniProtKB:  P17427
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SYNAPTOJANIN 1
P
12Homo sapiensMutation(s): 0 
Gene Names: SYNJ1 (KIAA0910)
EC: 3.1.3.36
Find proteins for O43426 (Homo sapiens)
Go to Gene View: SYNJ1
Go to UniProtKB:  O43426
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SYNAPTOJANIN 1
Q
12Homo sapiensMutation(s): 0 
Gene Names: SYNJ1 (KIAA0910)
EC: 3.1.3.36
Find proteins for O43426 (Homo sapiens)
Go to Gene View: SYNJ1
Go to UniProtKB:  O43426
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DTD
Query on DTD
Download SDF File 
Download CCD File 
A
DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
 Ligand Interaction
CO3
Query on CO3
Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
BEN
Query on BEN
Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.599α = 90.00
b = 67.322β = 94.53
c = 39.721γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance