4I0P Immune System date Nov 18, 2012
title Hla-Do In Complex With Hla-Dm
authors A.I.Guce, S.E.Mortimer, L.J.Stern
compound source
Molecule: Hla-Dma Protein
Chain: A, E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Homo Sapiens
Gene: 3108, Hla-Dma
Expression_system: Drosophila Melanogaster
Expression_system_taxid: 7227
Expression_system_strain: Schneider-2
Expression_system_vector_type: Plasmid

Molecule: Hla Class II Histocompatibility Antigen, Dm Beta
Chain: B, F
Synonym: Mhc Class II Antigen Dmb, Really Interesting New G Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Homo Sapiens
Gene: 3109, Dmb, Hla-Dmb, Ring7
Expression_system: Drosophila Melanogaster
Expression_system_taxid: 7227
Expression_system_strain: Schneider-2
Expression_system_vector_type: Plasmid

Molecule: Hla Class II Histocompatibility Antigen, Do Alpha
Chain: C, G
Synonym: Mhc Dn-Alpha, Mhc Dz Alpha, Mhc Class II Antigen D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Homo Sapiens
Gene: 3111, Hla-Dna, Hla-Doa, Hla-Dza
Expression_system: Drosophila Melanogaster
Expression_system_taxid: 7227
Expression_system_strain: Schneider-2
Expression_system_vector_type: Plasmid

Molecule: Hla Class II Histocompatibility Antigen, Do Beta
Chain: D, H
Synonym: Mhc Class II Antigen Dob
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Homo Sapiens
Gene: 3112, Hla-Dob
Expression_system: Drosophila Melanogaster
Expression_system_taxid: 7227
Expression_system_strain: Schneider-2
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.260 147.100 95.959 90.00 106.49 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand ACT, GOL, NAG, PGE enzyme
note 4I0P supersedes 3USA
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceHLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism., Guce AI, Mortimer SE, Yoon T, Painter CA, Jiang W, Mellins ED, Stern LJ, Nat Struct Mol Biol. 2012 Dec 9. doi: 10.1038/nsmb.2460. PMID:23222639
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (275 Kb) [Save to disk]
  • Biological Unit Coordinates (4i0p.pdb1.gz) 136 Kb
  • Biological Unit Coordinates (4i0p.pdb2.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 4I0P
  • CSU: Contacts of Structural Units for 4I0P
  • Structure Factors (274 Kb)
  • Retrieve 4I0P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I0P from S2C, [Save to disk]
  • Re-refined 4i0p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4I0P 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 4I0P
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4I0P, from MSDmotif at EBI
  • Fold representative 4i0p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i0p_E] [4i0p_C] [4i0p_F] [4i0p_A] [4i0p_H] [4i0p_D] [4i0p] [4i0p_B] [4i0p_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4I0P: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4I0P
  • Community annotation for 4I0P at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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