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: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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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
  • Primary Citation of Related Structures:  
    1W80

  • 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 domains, which are protein interaction hubs ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNITA250Mus musculusMutation(s): 0 
Gene Names: Ap2a2Adtab
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus)
Explore P17427 
Go to UniProtKB:  P17427
IMPC:  MGI:101920
Protein Feature View
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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)
Explore O43426 
Go to UniProtKB:  O43426
PHAROS:  O43426
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SYNAPTOJANIN 1C [auth Q]12Homo sapiensMutation(s): 0 
Gene Names: SYNJ1KIAA0910
EC: 3.1.3.36
UniProt & NIH Common Fund Data Resources
Find proteins for O43426 (Homo sapiens)
Explore O43426 
Go to UniProtKB:  O43426
PHAROS:  O43426
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 
H [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

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I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.599α = 90
b = 67.322β = 94.53
c = 39.721γ = 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: 2004-10-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance