1I3R Immune System date Feb 15, 2001
title Crystal Structure Of A Mutant Iek Class II Mhc Molecule
authors J.W.Kappler, N.Wilson
compound source
Molecule: H-2 Class II Histocompatibility Antigen, E-K Alph
Chain: A, C, E, G
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Iek
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Fusion Protein Consisting Of Mhc E-Beta-K Precurs Glycine Rich Linker, And Hemoglobin Beta-2 Chain;
Chain: B, D, F, H
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Iek
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.059 58.020 143.222 90.00 93.24 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NAG enzyme
related structures by homologous chain: 1JK8, 1KTD, 1T5W
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceMutations changing the kinetics of class II MHC peptide exchange., Wilson N, Fremont D, Marrack P, Kappler J, Immunity 2001 May;14(5):513-22. PMID:11371354
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (273 Kb) [Save to disk]
  • Biological Unit Coordinates (1i3r.pdb1.gz) 265 Kb
  • Biological Unit Coordinates (1i3r.pdb2.gz) 70 Kb
  • Biological Unit Coordinates (1i3r.pdb3.gz) 70 Kb
  • Biological Unit Coordinates (1i3r.pdb4.gz) 70 Kb
  • Biological Unit Coordinates (1i3r.pdb5.gz) 69 Kb
  • Biological Unit Coordinates (1i3r.pdb6.gz) 135 Kb
  • Biological Unit Coordinates (1i3r.pdb7.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 1I3R
  • CSU: Contacts of Structural Units for 1I3R
  • Likely Quarternary Molecular Structure file(s) for 1I3R
  • Retrieve 1I3R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1I3R from S2C, [Save to disk]
  • View 1I3R 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 1I3R
  • 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 1I3R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i3ra2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1i3ra1, region A:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rb2, region B:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rb1, region B:121-216 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rc2, region C:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rc1, region C:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rd2, region D:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rd1, region D:121-216 [Jmol] [rasmolscript] [script source]
        - Domain d1i3re2, region E:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1i3re1, region E:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rf2, region F:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rf1, region F:121-216 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rg2, region G:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rg1, region G:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rh2, region H:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1i3rh1, region H:121-216 [Jmol] [rasmolscript] [script source]
  • Fold representative 1i3r 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: [1i3r_D] [1i3r_C] [1i3r_A] [1i3r] [1i3r_F] [1i3r_E] [1i3r_G] [1i3r_B] [1i3r_H]
  • SWISS-PROT database: [P04224]
  • Domain organization of [HA22_MOUSE] by SWISSPFAM
  • Domains found in 1I3R: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 1I3R
  • Community annotation for 1I3R 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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