6D84

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1016/j.cell.2018.07.004
  • Primary Citation of Related Structures:  
    6CRI, 6D83, 6D84, 6DFF, 6CM9

  • 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 fact ...

    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; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jimhurley@berkeley.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bone marrow stromal antigen 2,Protein Nef LORT264Homo sapiensHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 2 
Gene Names: BST2nef
Find proteins for Q90VU7 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q90VU7
Find proteins for Q10589 (Homo sapiens)
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PHAROS:  Q10589
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit beta-1 BF586Homo sapiensMutation(s): 0 
Gene Names: AP1B1ADTB1BAM22CLAPB2
Find proteins for Q10567 (Homo sapiens)
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PHAROS:  Q10567
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor 1 CHIN193Homo sapiensMutation(s): 0 
Gene Names: ARF1
Find proteins for P84077 (Homo sapiens)
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PHAROS:  P84077
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1 GK601Mus musculusMutation(s): 0 
Gene Names: Ap1g1AdtgClapg1
Find proteins for P22892 (Mus musculus)
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IMPC:  MGI:101919
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1 MP423Mus musculusMutation(s): 0 
Gene Names: Ap1m1Cltnm
Find proteins for P35585 (Mus musculus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3 QS154Homo sapiensMutation(s): 0 
Gene Names: AP1S3
Find proteins for Q96PC3 (Homo sapiens)
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PHAROS:  Q96PC3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence