3VXR Immune System date Sep 20, 2012
title The Complex Between H27-14 Tcr And Hla-A24 Bound To Hiv-1 Ne 10(Wt) Peptide
authors A.Shimizu, S.Fukai, A.Yamagata, A.Iwamoto
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-24 Alph
Chain: A
Fragment: Unp Residues 25-298
Synonym: Aw-24, Hla Class I Histocompatibility Antigen, A-9 Chain, Mhc Class I Antigen A24;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-A
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d(+)

Molecule: Beta-2-Microglobulin
Chain: B
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a(+)

Molecule: H27-14 Tcr Alpha Chain
Chain: D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a(+)

Molecule: H27-14 Tcr Beta Chain
Chain: E
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d(+)

Molecule: 10-Mer Peptide From Protein Nef
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Other_details: Synthetic Peptide
symmetry Space Group: C 1 2 1
R_factor 0.199 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
221.447 47.740 113.994 90.00 119.91 90.00
method X-Ray Diffractionresolution 2.40 Å
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular response to iron io...

  • Primary referenceStructure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection., Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A, Sci Rep. 2013 Nov 6;3:3097. doi: 10.1038/srep03097. PMID:24192765
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (3vxr.pdb1.gz) 136 Kb
  • CSU: Contacts of Structural Units for 3VXR
  • Structure Factors (596 Kb)
  • Retrieve 3VXR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VXR from S2C, [Save to disk]
  • Re-refined 3vxr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VXR 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 3VXR
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3VXR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vxr_A] [3vxr_E] [3vxr_D] [3vxr_C] [3vxr_B] [3vxr]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3VXR: [IG_like] [IGc1] [IGv ] by SMART
  • Other resources with information on 3VXR
  • Community annotation for 3VXR at PDBWiki (http://pdbwiki.org)

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