3D25 Immune System date May 07, 2008
title Crystal Structure Of Ha-1 Minor Histocompatibility Antigen Bound To Human Class I Mhc Hla-A2
authors S.Nicholls, K.P.Piper, F.Mohammed, T.R.Dafforn, S.Tenzer, M.Salim, P.Mahendra, C.Craddock, P.Van Endert, H.Schild, M.Cobbold, V.H.Engelhard, P.A.H.Moss, B.E.Willcox
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain;
Chain: A
Synonym: Mhc Class I Antigen A2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-A, Hlaa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Beta-2-Microglobulin
Chain: B
Fragment: Unp Residues 22-119
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Nonameric Peptide From Ha-1
Chain: C
Fragment: Unp Residues 137-145
Synonym: Minor Histocompatibility Antigen Ha-1, Mhag Ha-1
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Is Commercially Synthesized. It Is Found Naturally In Humans.
symmetry Space Group: P 1 21 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.170 80.980 56.260 90.00 112.32 90.00
method X-Ray Diffractionresolution 1.30 Å
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular response to iron io...

  • Primary referenceSecondary anchor polymorphism in the HA-1 minor histocompatibility antigen critically affects MHC stability and TCR recognition., Nicholls S, Piper KP, Mohammed F, Dafforn TR, Tenzer S, Salim M, Mahendra P, Craddock C, van Endert P, Schild H, Cobbold M, Engelhard VH, Moss PA, Willcox BE, Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3889-94. Epub 2009 Feb 20. PMID:19234124
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (3d25.pdb1.gz) 145 Kb
  • CSU: Contacts of Structural Units for 3D25
  • Likely Quarternary Molecular Structure file(s) for 3D25
  • Structure Factors (811 Kb)
  • Retrieve 3D25 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D25 from S2C, [Save to disk]
  • Re-refined 3d25 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D25 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 3D25
  • 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 3D25, from MSDmotif at EBI
  • Fold representative 3d25 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d25] [3d25_A] [3d25_C] [3d25_B]
  • SWISS-PROT database: [P01892] [P61769] [Q92619]
  • Domain organization of [1A02_HUMAN] [B2MG_HUMAN] [HMHA1_HUMAN] by SWISSPFAM
  • Domain found in 3D25: [IGc1 ] by SMART
  • Other resources with information on 3D25
  • Community annotation for 3D25 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
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