OCA Atlas for 3FFC

3FFC

Immune System

date

Dec 03, 2008

title

Crystal Structure Of Cf34 Tcr In Complex With Hla-B8flr

authors

S.Gras, S.R.Burrows, L.Kjer-Nielsen, C.S.Clements, Y.C.Liu, L.C.S A.G.Brooks, A.W.Purcell, J.Mccluskey, J.Rossjohn

compound

source

Molecule: Hla Class I Histocompatibility Antigen, B-8 Alpha
Chain: A, F
Synonym: Mhc Class I Antigen B8
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-B, Hlab
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Beta-2-Microglobulin
Chain: B, G
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Flrgraygl Peptide From An Ebv Protein
Chain: C, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Cf34 Alpha Chain
Chain: D, I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Cf34 Beta Chain
Chain: E, J
Engineered: Yes

symmetry

Space Group: I 2 2 2

R_factor

0.221

R_Free

0.268

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
111.564	171.807	272.690	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.80 Å

ligand

CD, CL, NA

enzyme

Gene
Ontology

Chain	Function	Process	Component
G, B		cellular response to iron io...

Primary reference

The shaping of T cell receptor recognition by self-tolerance., Gras S, Burrows SR, Kjer-Nielsen L, Clements CS, Liu YC, Sullivan LC, Bell MJ, Brooks AG, Purcell AW, McCluskey J, Rossjohn J, Immunity. 2009 Feb 20;30(2):193-203. Epub 2009 Jan 22. PMID:19167249

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (277 Kb) [Save to disk]

Biological Unit Coordinates (3ffc.pdb1.gz) 137 Kb

Biological Unit Coordinates (3ffc.pdb2.gz) 138 Kb

LPC: Ligand-Protein Contacts for 3FFC

CSU: Contacts of Structural Units for 3FFC

Likely Quarternary Molecular Structure file(s) for 3FFC

Structure Factors (3688 Kb)

Retrieve 3FFC in mmCIF format [Save to disk]

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

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

View 3FFC 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 3FFC

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 3FFC, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ffc_H] [3ffc_E] [3ffc_G] [3ffc] [3ffc_J] [3ffc_A] [3ffc_D] [3ffc_I] [3ffc_F] [3ffc_B] [3ffc_C]

SWISS-PROT database: [P30460] [P61769] [P01848] [P01850]

Domain organization of [1B08_HUMAN] [B2MG_HUMAN] [TCA_HUMAN] [TCB_HUMAN] by SWISSPFAM

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

Other resources with information on 3FFC

Community annotation for 3FFC 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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