4P6Z Protein Transport date Mar 25, 2014
title Crystal Structure Of The Human Bst2 Cytoplasmic Domain And T Vpu Cytoplasmic Domain Bound To The Clathrin Adaptor Protei (Ap1) Core
authors X.Jia, Y.Xiong
compound source
Molecule: Ap-1 Complex Subunit Gamma-1
Chain: G
Fragment: Bst2tetheirn Cytoplasmic Domain, Unp Residues 1-
Synonym: Adapter-Related Protein Complex 1 Subunit Gamma-1, Protein Complex Ap-1 Subunit Gamma-1,Clathrin Assembly Prot Complex 1 Gamma-1 Large Chain,Gamma-Adaptin,Gamma1-Adaptin, Adaptor 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: 469008
Expression_system_strain: Bl21(De3)

Molecule: Ap-1 Complex Subunit Sigma-1a
Chain: S
Fragment: Hiv-1 Vpu Cytoplasmic Domain
Synonym: Adapter-Related Protein Complex 1 Subunit Sigma-1a Protein Complex Ap-1 Subunit Sigma-1a,Clathrin Assembly Pro Complex 1 Sigma-1a Small Chain,Clathrin Coat Assembly Prote Golgi Adaptor Ha1ap1 Adaptin Sigma-1a Subunit,Ha1 19 Kda S Sigma 1a Subunit Of Ap-1 Clathrin,Sigma-Adaptin 1a,Sigma1a-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ap1s1, Ap19, Claps1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Ap-1 Complex Subunit Mu-1
Chain: M
Fragment: Clathrin Adaptor Protein Complex 1 (Ap1) Core, Un 1-421;
Synonym: Ap-Mu Chain Family Member Mu1a,Adapter-Related Pro Complex 1 Subunit Mu-1,Adaptor Protein Complex Ap-1 Subunit Clathrin Assembly Protein Complex 1 Mu-1 Medium Chain 1,Cla Assembly Protein Ap47,Clathrin Coat-Associated Protein Ap47 Adaptor Ha1ap1 Adaptin Mu-1 Subunit,Mu-Adaptin 1,Mu1a-Adap
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Ap1m1, Cltnm
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Ap-1 Complex Subunit Beta-1
Chain: B
Fragment: Unp Residues 1-584
Synonym: Adapter-Related Protein Complex 1 Subunit Beta-1,A Protein Complex Ap-1 Subunit Beta-1,Beta-1-Adaptin,Beta-Ada Clathrin Assembly Protein Complex 1 Beta Large Chain,Golgi Ha1ap1 Adaptin Beta Subunit;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ap1b1, Adtb1, Bam22, Clapb2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Protein Vpu
Chain: V
Fragment: Unp Residues 21-81
Synonym: U Orf Protein,Viral Protein U
Engineered: Yes

Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B;
Organism_common: Hiv-1
Organism_taxid: 11691
Strain: Isolate Sf162
Gene: Vpu
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Bone Marrow Stromal Antigen 2
Chain: T
Fragment: Unp Residues 1-21
Synonym: Bst-2,Hm1.24 Antigen,Tetherin
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bst2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 43
R_factor 0.186 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
160.536 160.536 118.393 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
Gene
Ontology
ChainFunctionProcessComponent
B


G


M


S


V


Primary referenceStructural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1., Jia X, Weber E, Tokarev A, Lewinski M, Rizk M, Suarez M, Guatelli J, Xiong Y, Elife. 2014 Apr 29;3:e02362. doi: 10.7554/eLife.02362. PMID:24843023
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (585 Kb) [Save to disk]
  • Biological Unit Coordinates (4p6z.pdb1.gz) 576 Kb
  • CSU: Contacts of Structural Units for 4P6Z
  • Structure Factors (838 Kb)
  • Retrieve 4P6Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P6Z from S2C, [Save to disk]
  • Re-refined 4p6z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P6Z 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 4P6Z
  • 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
  • 3D motif for 4P6Z, from MSDmotif at EBI
  • Fold representative 4p6z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p6z_B] [4p6z_M] [4p6z_V] [4p6z] [4p6z_S] [4p6z_G] [4p6z_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4P6Z
  • Community annotation for 4P6Z at PDBWiki (http://pdbwiki.org)

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