4HMY

Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Recruitment and Activation of the AP-1 Clathrin Adaptor Complex by Arf1.

Ren, X.Farias, G.G.Canagarajah, B.J.Bonifacino, J.S.Hurley, J.H.

(2013) Cell 152: 755-767

  • DOI: https://doi.org/10.1016/j.cell.2012.12.042
  • Primary Citation of Related Structures:  
    4HMY

  • PubMed Abstract: 

    AP-1 is a clathrin adaptor complex that sorts cargo between the trans-Golgi network and endosomes. AP-1 recruitment to these compartments requires Arf1-GTP. The crystal structure of the tetrameric core of AP-1 in complex with Arf1-GTP, together with biochemical analyses, shows that Arf1 activates cargo binding by unlocking AP-1. Unlocking is driven by two molecules of Arf1 that bridge two copies of AP-1 at two interaction sites. The GTP-dependent switch I and II regions of Arf1 bind to the N terminus of the β1 subunit of one AP-1 complex, while the back side of Arf1 binds to the central part of the γ subunit trunk of a second AP-1 complex. A third Arf1 interaction site near the N terminus of the γ subunit is important for recruitment, but not activation. These observations lead to a model for the recruitment and activation of AP-1 by Arf1.


  • Organizational Affiliation

    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1601Mus musculusMutation(s): 0 
Gene Names: AdtgAp1g1Clapg1
UniProt & NIH Common Fund Data Resources
Find proteins for P22892 (Mus musculus)
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Go to UniProtKB:  P22892
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
AP-1 complex subunit beta-1586Homo sapiensMutation(s): 3 
Gene Names: ADTB1AP1B1BAM22CLAPB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q10567 (Homo sapiens)
Explore Q10567 
Go to UniProtKB:  Q10567
PHAROS:  Q10567
GTEx:  ENSG00000100280 
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UniProt GroupQ10567
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1C [auth M]423Mus musculusMutation(s): 0 
Gene Names: Ap1m1Cltnm
UniProt
Find proteins for P35585 (Mus musculus)
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Go to UniProtKB:  P35585
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UniProt GroupP35585
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3D [auth S]154Homo sapiensMutation(s): 1 
Gene Names: AP1S3
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Find proteins for Q96PC3 (Homo sapiens)
Explore Q96PC3 
Go to UniProtKB:  Q96PC3
PHAROS:  Q96PC3
GTEx:  ENSG00000152056 
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UniProt GroupQ96PC3
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1E [auth C]172Homo sapiensMutation(s): 1 
Gene Names: ARF1
UniProt & NIH Common Fund Data Resources
Find proteins for P84077 (Homo sapiens)
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Go to UniProtKB:  P84077
PHAROS:  P84077
GTEx:  ENSG00000143761 
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UniProt GroupP84077
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.5α = 90
b = 267.5β = 90
c = 191.4γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description