+Open data
-Basic information
Entry | Database: PDB / ID: 5e5m | ||||||
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Title | Crystal structure of mouse CTLA-4 in complex with nanobody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / treatment of metastatic melanomas | ||||||
Function / homology | Function and homology information CTLA4 inhibitory signaling / protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / clathrin-coated endocytic vesicle / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / positive regulation of apoptotic process ...CTLA4 inhibitory signaling / protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / clathrin-coated endocytic vesicle / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Camelidae (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.182 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Samanta, D. / Bonanno, J.B. / Almo, S.C. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of mouse CTLA-4 in complex with nanobody Authors: Fedorov, A.A. / Fedorov, E.V. / Samanta, D. / Bonanno, J.B. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e5m.cif.gz | 351.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5m.ent.gz | 300.5 KB | Display | PDB format |
PDBx/mmJSON format | 5e5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5m ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5m | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12927.545 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctla4, Cd152 / Production host: Escherichia coli (E. coli) / References: UniProt: P09793 #2: Antibody | Mass: 13685.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: Sodium/Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.182→19.969 Å / Num. obs: 98782 / % possible obs: 99.68 % / Redundancy: 4.1 % / Net I/σ(I): 7.4 |
-Processing
Software |
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Refinement | Resolution: 2.182→19.969 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 28.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.182→19.969 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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