OCA Atlas for 2F53

2F53

Immune System

date

Nov 25, 2005

title

Directed Evolution Of Human T-Cell Receptor Cdr2 Residues By Display Dramatically Enhances Affinity For Cognate Peptide- Without Apparent Cross-Reactivity

authors

P.J.Rizkallah, B.K.Jakobsen, S.M.Dunn, M.Sami

compound

source

Molecule: Hla Class I Histocompatibility Antigen
Chain: A
Fragment: Extracellular Domains Alpha 1, Alpha2 And Alpha3, 25-299;
Synonym: Mhc Class I Antigen A2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pex078

Molecule: Beta-2-Microglobulin
Chain: B
Fragment: Beta-2 Microglobulin, Residues 21-119
Engineered: Yes
Mutation: Yes

Molecule: Cancertestis Antigen 1b
Chain: C
Fragment: Residues 157-165
Synonym: L Antigen Family Member 2, Lage-2 Protein, Autoimm Cancertestis Antigen Ny-Eso-1;
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Homo Sapie (Humans);

Molecule: T-Cell Receptor, Alpha Chain
Chain: D
Engineered: Yes

Molecule: T-Cell Receptor, Beta Chain
Chain: E
Engineered: Yes

symmetry

Space Group: P 1 21 1

R_factor

0.166

R_Free

0.231

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
76.234	53.972	119.905	90.00	96.83	90.00

method

X-Ray Diffraction

resolution

2.10 Å

ligand

GOL, NA

enzyme

Gene
Ontology

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

Primary reference

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity., Dunn SM, Rizkallah PJ, Baston E, Mahon T, Cameron B, Moysey R, Gao F, Sami M, Boulter J, Li Y, Jakobsen BK, Protein Sci. 2006 Apr;15(4):710-21. PMID:16600963

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]

Biological Unit Coordinates (2f53.pdb1.gz) 146 Kb

Biological Unit Coordinates (2f53.pdb2.gz) 146 Kb

LPC: Ligand-Protein Contacts for 2F53

CSU: Contacts of Structural Units for 2F53

Likely Quarternary Molecular Structure file(s) for 2F53

Structure Factors (486 Kb)

Retrieve 2F53 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2F53 from S2C, [Save to disk]

Re-refined 2f53 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2F53 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 2F53

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 2F53, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2f53_E] [2f53] [2f53_D] [2f53_A] [2f53_C] [2f53_B]

SWISS-PROT database: [P01892] [P61769] [P78358] [P01848] [P01850]

Domain organization of [1A02_HUMAN] [B2MG_HUMAN] [CTG1B_HUMAN] [TCA_HUMAN] [TCB_HUMAN] by SWISSPFAM

Domains found in 2F53: [IG_like] [IGc1] [IGv ] by SMART

Other resources with information on 2F53

Community annotation for 2F53 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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