6CRI

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 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:  

  • 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 ...

    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.,Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: snowren@berkeley.edu.,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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bone marrow stromal antigen 2, Protein Nef chimera
T, N, c, Y, d, Z
264Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: nef, BST2
Find proteins for P03404 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03404
Find proteins for Q10589 (Homo sapiens)
Go to Gene View: BST2
Go to UniProtKB:  Q10589
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit beta-1
B, I, J
570Homo sapiensMutation(s): 2 
Gene Names: AP1B1 (ADTB1, BAM22, CLAPB2)
Find proteins for Q10567 (Homo sapiens)
Go to Gene View: AP1B1
Go to UniProtKB:  Q10567
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosylation factor 1
C, H, K, U, L, V
165Homo sapiensMutation(s): 1 
Gene Names: ARF1
Find proteins for P84077 (Homo sapiens)
Go to Gene View: ARF1
Go to UniProtKB:  P84077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit gamma-1
G, Q, R
585Mus musculusMutation(s): 0 
Gene Names: Ap1g1 (Adtg, Clapg1)
Find proteins for P22892 (Mus musculus)
Go to UniProtKB:  P22892
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit mu-1
M, W, X
422Mus musculusMutation(s): 0 
Gene Names: Ap1m1 (Cltnm)
Find proteins for P35585 (Mus musculus)
Go to UniProtKB:  P35585
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit sigma-3
S, a, b
142Homo sapiensMutation(s): 0 
Gene Names: AP1S3
Find proteins for Q96PC3 (Homo sapiens)
Go to Gene View: AP1S3
Go to UniProtKB:  Q96PC3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
C, H, K, L, U, V
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, H, K, L, U, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI 120691

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-08
    Type: Data collection, Database references