1IU1 | pdb_00001iu1

Crystal structure of human gamma1-adaptin ear domain

• PDB DOI: https://doi.org/10.2210/pdb1IU1/pdb

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


• Deposited: 2002-02-19 Released: 2002-07-10 
• Deposition Author(s): Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain.

Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K., Wakatsuki, S.

(2002) Nat Struct Biol 9: 527-531

• PubMed: 12042876 
• DOI: https://doi.org/10.1038/nsb808
• Primary Citation Related Structures: 
  1IU1


• PubMed Abstract: 
  

  The adaptor proteins AP-1 and GGA regulate membrane traffic between the trans-Golgi network (TGN) and endosomes/lysosomes through ARF-regulated membrane association, recognition of sorting signals, and recruitment of clathrin and accessory proteins. The gamma 1-adaptin subunits of AP-1 and GGA possess homologous ear domains involved in the recruitment of accessory proteins, gamma-synergin and Rabaptin-5. The crystal structure of the human gamma 1-adaptin ear domain consists solely of an immunoglobulin-like fold, unlike the alpha-adaptin ear domain. Structure-based mutational analyses reveal a binding site for the accessory proteins that is composed of conserved basic residues, indicating that the recruitment mechanism in gamma 1-adaptin and GGA is distinct from that in alpha-adaptin.

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Organizational Affiliation: 
• Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 32.27 kDa 
• Atom Count: 2,030 
• Modeled Residue Count: 243 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma1-adaptin	A, B	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43747 (Homo sapiens) Explore O43747  Go to UniProtKB:  O43747
PHAROS:  O43747 GTEx:  ENSG00000166747

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.132	α = 90
b = 62.132	β = 90
c = 147.869	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-10 
Deposition Author(s): Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K., Wakatsuki, S.

Revision History  

• Version 1.0: 2002-07-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-23
  Changes: Data collection, Database references
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references