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Yorodumi- PDB-6sru: Structure of Ig-like V-type domian of mouse Programmed cell death... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sru | ||||||
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Title | Structure of Ig-like V-type domian of mouse Programmed cell death 1 ligand 1 (PD-L1) | ||||||
Components | Programmed cell death 1 ligand 1 | ||||||
Keywords | IMMUNE SYSTEM / PD-L1 / immune checkpoint protein | ||||||
Function / homology | Function and homology information : / PD-1 signaling / positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...: / PD-1 signaling / positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / membrane => GO:0016020 / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / cell surface / signal transduction / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.532 Å | ||||||
Authors | Magiera-Mularz, K. / Sala, D. / Grudnik, P. / Holak, T.A. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Iscience / Year: 2021 Title: Human and mouse PD-L1: similar molecular structure, but different druggability profiles. Authors: Magiera-Mularz, K. / Kocik, J. / Musielak, B. / Plewka, J. / Sala, D. / Machula, M. / Grudnik, P. / Hajduk, M. / Czepiel, M. / Siedlar, M. / Holak, T.A. / Skalniak, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sru.cif.gz | 598.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sru.ent.gz | 501.9 KB | Display | PDB format |
PDBx/mmJSON format | 6sru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sru_validation.pdf.gz | 499 KB | Display | wwPDB validaton report |
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Full document | 6sru_full_validation.pdf.gz | 507.5 KB | Display | |
Data in XML | 6sru_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 6sru_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/6sru ftp://data.pdbj.org/pub/pdb/validation_reports/sr/6sru | HTTPS FTP |
-Related structure data
Related structure data | 5c3tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 13335.218 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd274, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EP73 #2: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 49.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M Tris pH 7.5, 20% PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978631 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978631 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→49.664 Å / Num. obs: 38622 / % possible obs: 94.1 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.53→2.62 Å / Rmerge(I) obs: 0.826 / Num. unique obs: 3645 / CC1/2: 0.567 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C3T Resolution: 2.532→49.664 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.24 Å2 / Biso mean: 67.5675 Å2 / Biso min: 29.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.532→49.664 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -25.5684 Å / Origin y: 9.7072 Å / Origin z: 17.0503 Å
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Refinement TLS group |
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