+Open data
-Basic information
Entry | Database: PDB / ID: 4mnh | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the DP10.7 TCR | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin / Histocompatibility antigens / T cell receptor / Immunological / lymphocytes / T cell recognition / activation / gamma delta T cell / Human / intraepithelial lymphocytes / CD1d / glycolipids / non-classical MHC / Glycoproteins / Cell-surface receptors | ||||||
Function / homology | Function and homology information cellular response to stimulus / positive regulation of phagocytosis / positive regulation of T cell activation / cell surface receptor signaling pathway / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Luoma, A.M. / Adams, E.J. | ||||||
Citation | Journal: Immunity / Year: 2013 Title: Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells. Authors: Luoma, A.M. / Castro, C.D. / Mayassi, T. / Bembinster, L.A. / Bai, L. / Picard, D. / Anderson, B. / Scharf, L. / Kung, J.E. / Sibener, L.V. / Savage, P.B. / Jabri, B. / Bendelac, A. / Adams, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4mnh.cif.gz | 173.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4mnh.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mnh_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4mnh_full_validation.pdf.gz | 470.5 KB | Display | |
Data in XML | 4mnh_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 4mnh_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/4mnh ftp://data.pdbj.org/pub/pdb/validation_reports/mn/4mnh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-Components
#1: Protein | Mass: 29284.555 Da / Num. of mol.: 2 Fragment: DP10.7 TCR gamma variable domain fused with human TCR beta constant domain Mutation: S173C, C191A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV3, TCRB, B2M, HDCMA22P, B2M, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K7N5M4 #2: Protein | Mass: 25402.463 Da / Num. of mol.: 2 Fragment: DP10.7 TCR delta variable domain fused with human TCR alpha constant domain Mutation: T167C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PJ56 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.31 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 20% PEG 10k, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 15411 / Num. obs: 15411 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % |
Reflection shell | Resolution: 3.3→3.36 Å / Mean I/σ(I) obs: 2.07 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→49.415 Å / SU ML: 0.48 / σ(F): 1.36 / Phase error: 32.12 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→49.415 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|