Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 31404.42 
• Atom Count: 2162 
• 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


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

---

Experimental Data Snapshot

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

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


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT	A	250	Mus musculus	Mutation(s): 0  Gene Names: Ap2a2 (Adtab)
Find proteins for P17427 (Mus musculus) Go to UniProtKB:  P17427

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
SYNAPTOJANIN 1	P	12	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
SYNAPTOJANIN 1	Q	12	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DTD	A	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
CO3	A	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
BEN	A	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

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 = 146.599	α = 90.00
b = 67.322	β = 94.53
c = 39.721	γ = 90.00

Software Package:

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

Structure Validation

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance