2NNA Immune System date Oct 24, 2006
title Structure Of The Mhc Class II Molecule Hla-Dq8 Bound With A Gluten Peptide
authors K.N.Henderson, J.A.Tye-Din, J.Rossjohn, R.P.Anderson
compound source
Molecule: Mhc Class II Antigen
Chain: A
Fragment: Residues In Database 24-207
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_strain: Hi5 Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbacdual

Molecule: Mhc Class II Antigen
Chain: B
Fragment: Residues In Database 33-224
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_strain: Hi5 Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbacdual

Molecule: Gluten Peptide
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: The C Terminus Of Chain C Was Linked To The Terminus Of Chain B With A Flexible Serine Glycine Linker. Flexible Linker Was Cleaved With Trypsin At An Unknown Poin Sequence During The Purification Process.
symmetry Space Group: P 21 21 21
R_factor 0.217 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.830 92.520 113.060 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceA structural and immunological basis for the role of human leukocyte antigen DQ8 in celiac disease., Henderson KN, Tye-Din JA, Reid HH, Chen Z, Borg NA, Beissbarth T, Tatham A, Mannering SI, Purcell AW, Dudek NL, van Heel DA, McCluskey J, Rossjohn J, Anderson RP, Immunity. 2007 Jul;27(1):23-34. Epub 2007 Jul 12. PMID:17629515
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (2nna.pdb1.gz) 69 Kb
  • CSU: Contacts of Structural Units for 2NNA
  • Likely Quarternary Molecular Structure file(s) for 2NNA
  • Structure Factors (274 Kb)
  • Retrieve 2NNA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NNA from S2C, [Save to disk]
  • Re-refined 2nna structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NNA 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 2NNA
  • 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 2NNA, from MSDmotif at EBI
  • Fold representative 2nna from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nna_C] [2nna_B] [2nna_A] [2nna]
  • SWISS-PROT database: [P01909] [P01920] [P18573]
  • Domain organization of [DQA1_HUMAN] [DQB1_HUMAN] [GDA9_WHEAT] by SWISSPFAM
  • Domains found in 2NNA: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 2NNA with the sequences similar proteins can be viewed for 2NNA's classification [DQA1_HUMAN] [DQB1_HUMAN] [GDA9_WHEAT] 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] [GDA9_WHEAT] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2NNA
  • Community annotation for 2NNA 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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