1JK8	Immune System	date	Jul 11, 2001
title	Crystal Structure Of A Human Insulin Peptide-Hla-Dq8 Complex
authors	K.H.Lee, K.W.Wucherpfennig, D.C.Wiley
compound		source
Molecule: Mhc Class II Hla-Dq8 Chain: A Fragment: Alpha Chain (Dqa10301) Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_vector_type: Baculovirus
Molecule: Mhc Class II Hla-Dq8 Chain: B Fragment: Beta Chain (Dqb10302) Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_vector_type: Baculovirus
Molecule: Insulin B Peptide Chain: C Fragment: Peptide (9-Shlvealylvcgerg-23) Engineered: Yes		Synthetic: Yes Other_details: This Peptide Was Chemically Synthesized. The Of This Peptide Occurs Naturally In Humans (Homo Sapiens).
symmetry	Space Group: P 1 21 1	R_factor 0.224 R_Free 0.258
crystal cell	length a length b length c angle alpha angle beta angle gamma 66.034 42.862 87.467 90.00 102.48 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	NAG	enzyme
related structures	by homologous chain: 1I3R, 1KTD, 1S9V, 2IAD
Primary reference	Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes., Lee KH, Wucherpfennig KW, Wiley DC, Nat Immunol 2001 Jun;2(6):501-7. PMID:11376336

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk] Biological Unit Coordinates (1jk8.pdb1.gz) 65 Kb LPC: Ligand-Protein Contacts for 1JK8 CSU: Contacts of Structural Units for 1JK8 Likely Quarternary Molecular Structure file(s) for 1JK8 Structure Factors (149 Kb) Retrieve 1JK8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1JK8 from S2C, [Save to disk] Re-refined 1jk8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1JK8 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1JK8

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 1JK8, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1jk8a2, region A:2-84 [Jmol] [rasmolscript] [script source]     - Domain d1jk8a1, region A:85-181 [Jmol] [rasmolscript] [script source]     - Domain d1jk8b2, region B:3-94 [Jmol] [rasmolscript] [script source]     - Domain d1jk8b1, region B:95-192 [Jmol] [rasmolscript] [script source] Fold representative 1jk8 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: [1jk8_A] [1jk8_B] [1jk8_C] SWISS-PROT database: [P01909] [P01920] Domain organization of [DQA1_HUMAN] [DQB1_HUMAN] by SWISSPFAM Domains found in 1JK8: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1JK8 with the sequences similar proteins can be viewed for 1JK8's classification [DQA1_HUMAN] [DQB1_HUMAN] 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 [DQA1_HUMAN] [DQB1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1JK8

Community annotation for 1JK8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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