1E42

Beta2-adaptin appendage domain, from clathrin adaptor AP2

• PDB DOI: https://doi.org/10.2210/pdb1E42/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-06-27 Released: 2000-08-21 
• Deposition Author(s): Owen, D.J., Evans, P.R., McMahon, H.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 

Literature

The Structure and Function of the Beta2-Adaptin Appendage Domain

Owen, D.J., Vallis, Y., Pearse, B.M.F., Mcmahon, H.T., Evans, P.R.

(2000) EMBO J 19: 4216

• PubMed: 10944104 
• DOI: https://doi.org/10.1093/emboj/19.16.4216
• Primary Citation of Related Structures:  
  1E42


• PubMed Abstract: 
  

  The heterotetrameric AP2 adaptor (alpha, beta 2, mu 2 and sigma 2 subunits) plays a central role in clathrin-mediated endocytosis. We present the protein recruitment function and 1.7 A resolution structure of its beta 2-appendage domain to complement those previously determined for the mu 2 subunit and alpha appendage. Using structure-directed mutagenesis, we demonstrate the ability of the beta 2 appendage alone to bind directly to clathrin and the accessory proteins AP180, epsin and eps15 at the same site. Clathrin polymerization is promoted by binding of clathrin simultaneously to the beta 2-appendage site and to a second site on the adjacent beta 2 hinge. This results in the displacement of the other ligands from the beta 2 appendage. Thus clathrin binding to an AP2-accessory protein complex would cause the controlled release of accessory proteins at sites of vesicle formation.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.96 kDa 
• Atom Count: 4,555 
• Modelled Residue Count: 466 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 COMPLEX SUBUNIT BETA	A, B	258	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P63010 (Homo sapiens) Explore P63010  Go to UniProtKB:  P63010
PHAROS:  P63010 GTEx:  ENSG00000006125

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTD	C [auth A], H [auth B]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
GOL	G [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A], F [auth A], M [auth B], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.04	α = 90
b = 124.59	β = 124.18
c = 67.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-21 
Deposition Author(s): Owen, D.J., Evans, P.R., McMahon, H.T.

Revision History  

• Version 1.0: 2000-08-21
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other