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Yorodumi- PDB-5tru: Structure of the first-in-class checkpoint inhibitor Ipilimumab b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tru | ||||||
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Title | Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / complex / Fab | ||||||
Function / homology | Function and homology information protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / 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 ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ramagopal, U.A. / Liu, W. / Garrett-Thomson, S.C. / Yan, Q. / Srinivasan, M. / Wong, S.C. / Bell, A. / Mankikar, S. / Rangan, V.S. / Deshpande, S. ...Ramagopal, U.A. / Liu, W. / Garrett-Thomson, S.C. / Yan, Q. / Srinivasan, M. / Wong, S.C. / Bell, A. / Mankikar, S. / Rangan, V.S. / Deshpande, S. / Bonanno, J.B. / Korman, A.J. / Almo, S.C. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural basis for cancer immunotherapy by the first-in-class checkpoint inhibitor ipilimumab. Authors: Ramagopal, U.A. / Liu, W. / Garrett-Thomson, S.C. / Bonanno, J.B. / Yan, Q. / Srinivasan, M. / Wong, S.C. / Bell, A. / Mankikar, S. / Rangan, V.S. / Deshpande, S. / Korman, A.J. / 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 | 5tru.cif.gz | 409.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tru.ent.gz | 341.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tru_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 5tru_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 5tru_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 5tru_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/5tru ftp://data.pdbj.org/pub/pdb/validation_reports/tr/5tru | HTTPS FTP |
-Related structure data
Related structure data | 1i85S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23477.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 24232.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Protein | Mass: 12637.422 Da / Num. of mol.: 2 / Fragment: UNP residues 37-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P16410 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→34.91 Å / Num. obs: 28514 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.143 / Χ2: 1.208 / Net I/av σ(I): 14.6 / Net I/σ(I): 6.1 / Num. measured all: 181876 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I85 Resolution: 3→34.91 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.885 / SU B: 51.86 / SU ML: 0.396 / SU R Cruickshank DPI: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.447 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.11 Å2 / Biso mean: 69.607 Å2 / Biso min: 44 Å2
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Refinement step | Cycle: final / Resolution: 3→34.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.998→3.075 Å / Total num. of bins used: 20
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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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