OCA Atlas for 3ARD

3ARD

Immune System

date

Nov 27, 2010

title

Ternary Crystal Structure Of The Mouse Nkt Tcr-Cd1d-3'Deoxy- Galactosylceramide

authors

K.S.Wun, J.Rossjohn

compound

source

Molecule: Antigen-Presenting Glycoprotein Cd1d1
Chain: A
Fragment: Heavy Chain
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Cd1d1, Cd1.1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pbacp10ph

Molecule: Beta-2-Microglobulin
Chain: B
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: B2m
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pbacp10ph

Molecule: Nkt Valpha14-Jalpha18,Nkt Valpha14-Jalpha18
Chain: C
Engineered: Yes
Other_details: Chimera Of Mouse Variable Domain And Human C Domain,Chimera Of Mouse Variable Domain And Human Constant

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Vbeta8.2,Vbeta8.2
Chain: D
Engineered: Yes
Other_details: Chimera Of Mouse Variable Domain And Human C Domain,Chimera Of Mouse Variable Domain And Human Constant

symmetry

Space Group: P 21 21 21

R_factor

0.213

R_Free

0.277

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
58.991	86.732	235.198	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.01 Å

ligand

3GH, NAG

enzyme

Gene
Ontology

Chain	Function	Process	Component
B

Primary reference

A Molecular Basis for the Exquisite CD1d-Restricted Antigen Specificity and Functional Responses of Natural Killer T Cells., Wun KS, Cameron G, Patel O, Pang SS, Pellicci DG, Sullivan LC, Keshipeddy S, Young MH, Uldrich AP, Thakur MS, Richardson SK, Howell AR, Illarionov PA, Brooks AG, Besra GS, McCluskey J, Gapin L, Porcelli SA, Godfrey DI, Rossjohn J, Immunity. 2011 Mar 25;34(3):327-39. Epub 2011 Mar 3. PMID:21376639

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (280 Kb) [Save to disk]

Biological Unit Coordinates (3ard.pdb1.gz) 272 Kb

LPC: Ligand-Protein Contacts for 3ARD

CSU: Contacts of Structural Units for 3ARD

Structure Factors (1361 Kb)

Retrieve 3ARD in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3ARD from S2C, [Save to disk]

Re-refined 3ard structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ARD 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 3ARD

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

3D motif for 3ARD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ard_C] [3ard_A] [3ard_B] [3ard] [3ard_D]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3ARD: [IG] [IG_like] [IGc1] [IGv ] by SMART

Other resources with information on 3ARD

Community annotation for 3ARD 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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