1R5I Immune System date Oct 10, 2003
title Crystal Structure Of The Mam-Mhc Complex
authors Y.Zhao, Z.Li, S.J.Drozd, Y.Guo, W.Mourad, H.Li
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain;
Chain: A, E
Fragment: Alpha Chain Of Class II Mhc (Residues 26-206)
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain;
Chain: B, F
Fragment: Beta Chain Of Class II Mhc (Residues 30-219)
Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: Hemagglutinin Peptide
Chain: C, G
Fragment: Haemagglutinin Peptide (Residues 306-318)
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. This Sequence Occurs Naturally In Influenza Virus.;

Molecule: Superantigen
Chain: D, H
Synonym: Mycoplasma Arthritidis-Derived Mitogen
Engineered: Yes

Organism_scientific: Mycoplasma Arthritidis
Organism_taxid: 2111
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: I 2 2 2
R_factor 0.238 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.286 178.814 179.554 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand MSE, PO4 enzyme
related structures by homologous chain: 1BX2, 1FYT, 1KG0
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B


Primary referenceCrystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex., Zhao Y, Li Z, Drozd SJ, Guo Y, Mourad W, Li H, Structure (Camb) 2004 Feb;12(2):277-88. PMID:14962388
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (1r5i.pdb1.gz) 104 Kb
  • Biological Unit Coordinates (1r5i.pdb2.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 1R5I
  • CSU: Contacts of Structural Units for 1R5I
  • Likely Quarternary Molecular Structure file(s) for 1R5I
  • Structure Factors (635 Kb)
  • Retrieve 1R5I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R5I from S2C, [Save to disk]
  • Re-refined 1r5i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1R5I 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 1R5I
  • 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 1R5I, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r5ia2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1r5ia1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1r5ib2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1r5ib1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1r5id_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1r5ie2, region E:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1r5ie1, region E:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1r5if2, region F:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1r5if1, region F:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1r5ih_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1r5i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r5i_G] [1r5i_D] [1r5i] [1r5i_C] [1r5i_B] [1r5i_E] [1r5i_H] [1r5i_A] [1r5i_F]
  • SWISS-PROT database: [P04229] [P01903] [P11133] [Q48898]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [HEMA_I78A9] [Q48898_MYCAT] by SWISSPFAM
  • Domains found in 1R5I: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1R5I with the sequences similar proteins can be viewed for 1R5I's classification [2B11_HUMAN] [DRA_HUMAN] [HEMA_I78A9] [Q48898_MYCAT] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [2B11_HUMAN] [DRA_HUMAN] [HEMA_I78A9] [Q48898_MYCAT] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1R5I
  • Community annotation for 1R5I at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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