1GYW | pdb_00001gyw

Gamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant

• PDB DOI: https://doi.org/10.2210/pdb1GYW/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Mus musculus
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2002-04-30 Released: 2002-08-22 
• Deposition Author(s): Evans, P.R., Miele, A.E., Owen, D.J., McMahon, H.M., Kent, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Gamma-adaptin appendage domain: structure and binding site for Eps15 and gamma-synergin.

Kent, H.M., McMahon, H.T., Evans, P.R., Benmerah, A., Owen, D.J.

(2002) Structure 10: 1139-1148

• PubMed: 12176391 
• DOI: https://doi.org/10.1016/s0969-2126(02)00801-8
• Primary Citation Related Structures: 
  1GYU, 1GYV, 1GYW


• PubMed Abstract: 
  

  The AP1 complex is one of a family of heterotetrameric clathrin-adaptor complexes involved in vesicular trafficking between the Golgi and endosomes. The complex has two large subunits, gamma and beta1, which can be divided into trunk, hinge, and appendage domains. The 1.8 A resolution structure of the gamma appendage is presented. The binding site for the known gamma appendage ligand gamma-synergin is mapped through creation of point mutations designed on the basis of the structure. We also show that Eps15, a protein believed to be involved in vesicle formation at the plasma membrane, is also a ligand of gamma appendage and binds to the same site as gamma-synergin. This observation explains the demonstrated brefeldinA (BFA)-sensitive colocalization of Eps15 and AP1 at the Golgi complex.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 28.55 kDa 
• Atom Count: 2,172 
• Modeled Residue Count: 254 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT	A, B	128	Mus musculus	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P22892 (Mus musculus) Explore P22892  Go to UniProtKB:  P22892
IMPC:  MGI:101919

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.155	α = 90
b = 62.155	β = 90
c = 148.903	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-22 
Deposition Author(s): Evans, P.R., Miele, A.E., Owen, D.J., McMahon, H.M., Kent, H.M.

Revision History  

• Version 1.0: 2002-08-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Database references, Source and taxonomy
• Version 1.4: 2019-03-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-10-09
  Changes: Data collection, Database references, Other
• Version 1.6: 2023-12-13
  Changes: Data collection, Database references, Refinement description