Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 31.40 kDa 
• Atom Count: 2439 
• Modelled Residue Count: 264 
• Deposited Residue Count: 274 
• Unique protein chains: 3

1W80

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

• DOI: 10.2210/pdb1W80/pdb

• Classification: ENDOCYTOSIS/EXOCYTOSIS
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-09-14 Released: 2004-10-27 
• Deposition Author(s): Ford, M.G.J., Praefcke, G.J.K., McMahon, H.T.

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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 

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

• PubMed: 15496985 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT	A	250	Mus musculus	Mutation(s): 0  Gene Names: Ap2a2, Adtab
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus) Explore P17427  Go to UniProtKB:  P17427
IMPC:  MGI:101920

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPTOJANIN 1	B [auth P]	12	Homo sapiens	Mutation(s): 0  Gene Names: SYNJ1, KIAA0910 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 GTEx:  ENSG00000159082

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPTOJANIN 1	C [auth Q]	12	Homo sapiens	Mutation(s): 0  Gene Names: SYNJ1, KIAA0910 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 GTEx:  ENSG00000159082

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTD (Subject of Investigation/LOI)	H [auth A]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
BEN	D [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO3	E [auth A], F [auth A], G [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

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 = 146.599	α = 90
b = 67.322	β = 94.53
c = 39.721	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2004-09-14 
• Released Date: 2004-10-27 
Deposition Author(s): Ford, M.G.J., Praefcke, G.J.K., McMahon, H.T.

Revision History  

• 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