OCA Atlas for 2NNA

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

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 Diffraction

resolution

2.10 Å

Primary reference

A 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.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2nna_B] [2nna_C]

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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