8D4D

gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat.

Hooy, R.M.Iwamoto, Y.Tudorica, D.A.Ren, X.Hurley, J.H.

(2022) Sci Adv 8: eadd3914-eadd3914

  • DOI: https://doi.org/10.1126/sciadv.add3914
  • Primary Citation of Related Structures:  
    7UX3, 8D4C, 8D4D, 8D4E, 8D4F, 8D4G, 8D9R, 8D9S, 8D9T, 8D9U, 8D9V, 8D9W

  • PubMed Abstract: 

    The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1A [auth C],
B [auth H],
J [auth D],
K [auth F]
180Homo sapiensMutation(s): 0 
Gene Names: ARF1
UniProt & NIH Common Fund Data Resources
Find proteins for P84077 (Homo sapiens)
Go to UniProtKB:  P84077
PHAROS:  P84077
GTEx:  ENSG00000143761 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NefC [auth N],
G [auth L],
L [auth K],
P [auth I]
212Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: nef
UniProt
Find proteins for Q90VU7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q90VU7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A alpha chainD [auth Y],
M [auth P]
39Homo sapiensMutation(s): 4 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit beta-1E [auth B],
N [auth A]
949Homo sapiensMutation(s): 2 
Gene Names: AP1B1ADTB1BAM22CLAPB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q10567 (Homo sapiens)
Go to UniProtKB:  Q10567
PHAROS:  Q10567
GTEx:  ENSG00000100280 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1F [auth G],
O [auth E]
601Mus musculusMutation(s): 0 
Gene Names: Ap1g1AdtgClapg1
UniProt & NIH Common Fund Data Resources
Find proteins for P22892 (Mus musculus)
Go to UniProtKB:  P22892
IMPC:  MGI:101919
Sequence Annotations
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1H [auth M],
Q [auth J]
423Mus musculusMutation(s): 0 
Gene Names: Ap1m1Cltnm
UniProt
Find proteins for P35585 (Mus musculus)
Go to UniProtKB:  P35585
Sequence Annotations
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  • Reference Sequence
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3I [auth S],
R [auth O]
154Homo sapiensMutation(s): 0 
Gene Names: AP1S3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PC3 (Homo sapiens)
Go to UniProtKB:  Q96PC3
PHAROS:  Q96PC3
GTEx:  ENSG00000152056 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
S [auth C],
U [auth H],
W [auth D],
Y [auth F]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
T [auth C],
V [auth H],
X [auth D],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20-4459
RECONSTRUCTIONRELION3.1.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF32 AI152971
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI120691
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50 AI150476

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection, Refinement description