6CM9

Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.

Morris, K.L.Buffalo, C.Z.Sturzel, C.M.Heusinger, E.Kirchhoff, F.Ren, X.Hurley, J.H.

(2018) Cell 174: 659-671.e14

  • DOI: https://doi.org/10.1016/j.cell.2018.07.004
  • Primary Citation of Related Structures:  
    6CM9, 6CRI, 6D83, 6D84, 6DFF

  • PubMed Abstract: 

    The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.


  • Organizational Affiliation

    Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bone marrow stromal antigen 2, Protein Nef chimeraA [auth L],
B [auth T],
I [auth N]
264Homo sapiensHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
Gene Names: BST2nef
UniProt & NIH Common Fund Data Resources
Find proteins for Q90VU7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q90VU7
Find proteins for Q10589 (Homo sapiens)
Go to UniProtKB:  Q10589
PHAROS:  Q10589
GTEx:  ENSG00000130303 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit beta-1C [auth B]586Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 1D [auth C],
F [auth H]
193Homo sapiensMutation(s): 1 
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1E [auth G]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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1G [auth M]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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3H [auth S]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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.13

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 StatesR01 AI 120691

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description