6D84 Protein Transport date Apr 25, 2018
title Structure Of The Cargo Bound Ap-1:Arf1:Tetherin-Nef (L164a, Dileucine Mutant Dimer
authors C.Z.Buffalo, K.L.Morris, J.H.Hurley
compound source
Molecule: Bone Marrow Stromal Antigen 2,Protein Nef
Chain: T, L, R, O
Fragment: Tetherin Unp Residues 2-21, Nef Unp Residues 1-20
Synonym: Bst-2,Hm1.24 Antigen,Tetherin,3'Orf,Negative Facto Protein;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens, Human Immunodeficiency V
Organism_common: Human
Organism_taxid: 9606, 11676
Gene: Bst2, Nef
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ap-1 Complex Subunit Beta-1
Chain: B, F
Synonym: Adaptor Protein Complex Ap-1 Subunit Beta-1,Adapto Protein Complex 1 Subunit Beta-1,Beta-1-Adaptin,Beta-Adapti Clathrin Assembly Protein Complex 1 Beta Large Chain,Golgi Ha1ap1 Adaptin Beta Subunit;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ap1b1, Adtb1, Bam22, Clapb2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Adp-Ribosylation Factor 1
Chain: C, H, I, N
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Arf1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ap-1 Complex Subunit Gamma-1
Chain: G, K
Synonym: Adaptor Protein Complex Ap-1 Subunit Gamma-1,Adapt Protein Complex 1 Subunit Gamma-1,Clathrin Assembly Protein Gamma-1 Large Chain,Gamma-Adaptin,Gamma1-Adaptin,Golgi Adap Ha1ap1 Adaptin Subunit Gamma-1;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Ap1g1, Adtg, Clapg1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ap-1 Complex Subunit Mu-1
Chain: M, P
Synonym: Ap-Mu Chain Family Member Mu1a,Adaptor Protein Com Subunit Mu-1,Adaptor-Related Protein Complex 1 Subunit Mu-1 Assembly Protein Complex 1 Mu-1 Medium Chain 1,Clathrin Coa Protein Ap47,Clathrin Coat-Associated Protein Ap47,Golgi Ad Ha1ap1 Adaptin Mu-1 Subunit,Mu-Adaptin 1,Mu1a-Adaptin;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Ap1m1, Cltnm
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ap-1 Complex Subunit Sigma-3
Chain: S, Q
Synonym: Adaptor Protein Complex Ap-1 Subunit Sigma-1c,Adap Related Protein Complex 1 Subunit Sigma-1c,Clathrin Assembl Complex 1 Sigma-1c Small Chain,Golgi Adaptor Ha1ap1 Adapti Subunit,Sigma 1c Subunit Of Ap-1 Clathrin,Sigma-Adaptin 1c, Adaptin;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ap1s3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 6.72 Å
Gene
Ontology
ChainFunctionProcessComponent
F, B


K, G


N, H, C, I
  • phospholipase D activator ac...


  • O, T, R, L


    P, M


    S, Q


    Primary referenceHIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation., Morris KL, Buffalo CZ, Sturzel CM, Heusinger E, Kirchhoff F, Ren X, Hurley JH, Cell. 2018 Jul 26;174(3):659-671.e14. doi: 10.1016/j.cell.2018.07.004. PMID:30053425
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (616 Kb) [Save to disk]
  • Biological Unit Coordinates (6d84.pdb1.gz) 602 Kb
  • CSU: Contacts of Structural Units for 6D84
  • Retrieve 6D84 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D84 from S2C, [Save to disk]
  • View 6D84 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6D84
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6d84 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d84_K] [6d84_S] [6d84_M] [6d84_T] [6d84_F] [6d84_H] [6d84_Q] [6d84_I] [6d84_P] [6d84_N] [6d84_R] [6d84_L] [6d84_C] [6d84_G] [6d84_B] [6d84_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D84
  • Community annotation for 6D84 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science