1W63 | pdb_00001w63

AP1 clathrin adaptor core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.310 (Depositor) 
  • R-Value Work: 
    0.297 (Depositor) 
  • R-Value Observed: 
    0.297 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of the Clathrin Adaptor Protein 1 Core

Heldwein, E.Macia, E.Wang, J.Yin, H.L.Kirchhausen, T.Harrison, S.C.

(2004) Proc Natl Acad Sci U S A 101: 14108

  • DOI: https://doi.org/10.1073/pnas.0406102101
  • Primary Citation Related Structures: 
    1W63

  • PubMed Abstract: 

    The heterotetrameric adaptor proteins (AP complexes) link the outer lattice of clathrin-coated vesicles with membrane-anchored cargo molecules. We report the crystal structure of the core of the AP-1 complex, which functions in the trans-Golgi network (TGN). Packing of complexes in the crystal generates an exceptionally long (1,135-A) unit-cell axis, but the 6-fold noncrystallographic redundancy yields an excellent map at 4-A resolution. The AP-1 core comprises N-terminal fragments of the two large chains, beta1 and gamma, and the intact medium and small chains, micro1 and sigma1. Its molecular architecture closely resembles that of the core of AP-2, the plasma-membrane-specific adaptor, for which a structure has been determined. Both structures represent an "inactive" conformation with respect to binding of cargo with a tyrosine-based sorting signal. TGN localization of AP-1 depends on the small GTPase, Arf1, and the phosphoinositide, PI-4-P. We show that directed mutations of residues at a particular corner of the gamma chain prevent recruitment to the TGN in cells and diminish PI-4-P-dependent, but not Arf1-dependent, liposome binding in vitro.


  • Organizational Affiliation
    • Children's Hospital, Howard Hughes Medical Institute, Department of Cell Biology, and CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 1,218.98 kDa 
  • Atom Count: 81,744 
  • Modeled Residue Count: 10,218 
  • Deposited Residue Count: 10,698 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
A, C, E, G, I
A, C, E, G, I, K
618Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P22892 (Mus musculus)
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IMPC:  MGI:101919
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UniProt GroupP22892
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT
B, D, F, H, J
B, D, F, H, J, L
584Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P52303 (Rattus norvegicus)
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Go to UniProtKB:  P52303
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UniProt GroupP52303
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT
M, N, O, P, R
M, N, O, P, R, V
423Mus musculusMutation(s): 0 
UniProt
Find proteins for P35585 (Mus musculus)
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UniProt GroupP35585
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT
Q, S, T, U, W
Q, S, T, U, W, X
158Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61967 (Mus musculus)
Explore P61967 
Go to UniProtKB:  P61967
IMPC:  MGI:1098244
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UniProt GroupP61967
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free:  0.310 (Depositor) 
  • R-Value Work:  0.297 (Depositor) 
  • R-Value Observed: 0.297 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.14α = 90
b = 178.14β = 90
c = 1134.994γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-21
    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: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description