Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 16-mer - A4B2C2D2E2F2G2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A4B2C2D2E2F1G1H1I1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, microscopy

Macromolecule Content

• Total Structure Weight: 613.52 kDa 
• Atom Count: 33176 
• Residue Count: 4126 
• Unique protein chains: 6

6D84

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

• DOI: 10.2210/pdb6D84/pdb
• EMDataResource: EMD-7454

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens, Human immunodeficiency virus 1, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-04-25 Released: 2018-08-08 
• Deposition Author(s): Buffalo, C.Z., Morris, K.L., Hurley, J.H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

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

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

• PubMed: 30053425 
• 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 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone marrow stromal antigen 2,Protein Nef	L, O, R, T	264	Homo sapiens, Human immunodeficiency virus 1 This entity is chimeric	Mutation(s): 2  Gene Names: BST2, nef
Find proteins for Q90VU7 (Human immunodeficiency virus 1) Explore Q90VU7  Go to UniProtKB:  Q90VU7
Find proteins for Q10589 (Homo sapiens) Explore Q10589  Go to UniProtKB:  Q10589
NIH Common Fund Data Resources
PHAROS:  Q10589 GTEx:  ENSG00000130303

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit beta-1	B, F	586	Homo sapiens	Mutation(s): 0  Gene Names: AP1B1, ADTB1, BAM22, CLAPB2
Find proteins for Q10567 (Homo sapiens) Explore Q10567  Go to UniProtKB:  Q10567
NIH Common Fund Data Resources
PHAROS:  Q10567 GTEx:  ENSG00000100280

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 1	C, H, I, N	193	Homo sapiens	Mutation(s): 0  Gene Names: ARF1
Find proteins for P84077 (Homo sapiens) Explore P84077  Go to UniProtKB:  P84077
NIH Common Fund Data Resources
PHAROS:  P84077 GTEx:  ENSG00000143761

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit gamma-1	G, K	601	Mus musculus	Mutation(s): 0  Gene Names: Ap1g1, Adtg, Clapg1
Find proteins for P22892 (Mus musculus) Explore P22892  Go to UniProtKB:  P22892
NIH Common Fund Data Resources
IMPC:  MGI:101919

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit mu-1	M, P	423	Mus musculus	Mutation(s): 0  Gene Names: Ap1m1, Cltnm
Find proteins for P35585 (Mus musculus) Explore P35585  Go to UniProtKB:  P35585

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit sigma-3	Q, S	154	Homo sapiens	Mutation(s): 0  Gene Names: AP1S3
Find proteins for Q96PC3 (Homo sapiens) Explore Q96PC3  Go to UniProtKB:  Q96PC3
NIH Common Fund Data Resources
PHAROS:  Q96PC3 GTEx:  ENSG00000152056

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C, H, I, N	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	C, H, I, N	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-04-25 
• Released Date: 2018-08-08 
Deposition Author(s): Buffalo, C.Z., Morris, K.L., Hurley, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI 120691

Revision History 

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