+Open data
-Basic information
Entry | Database: PDB / ID: 5mgr | |||||||||
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Title | Human receptor NKR-P1 in glycosylated form, extracellular domain | |||||||||
Components | Killer cell lectin-like receptor subfamily B member 1 | |||||||||
Keywords | IMMUNE SYSTEM / receptor / CTL fold / natural killer cell | |||||||||
Function / homology | Function and homology information regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / cell surface / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Skalova, T. / Blaha, J. / Stransky, J. / Koval, T. / Hasek, J. / Yuguang, Z. / Harlos, K. / Vanek, O. / Dohnalek, J. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse. Authors: Blaha, J. / Skalova, T. / Kalouskova, B. / Skorepa, O. / Cmunt, D. / Grobarova, V. / Pazicky, S. / Polachova, E. / Abreu, C. / Stransky, J. / Koval, T. / Duskova, J. / Zhao, Y. / Harlos, K. ...Authors: Blaha, J. / Skalova, T. / Kalouskova, B. / Skorepa, O. / Cmunt, D. / Grobarova, V. / Pazicky, S. / Polachova, E. / Abreu, C. / Stransky, J. / Koval, T. / Duskova, J. / Zhao, Y. / Harlos, K. / Hasek, J. / Dohnalek, J. / Vanek, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mgr.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgr.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgr ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgr | HTTPS FTP |
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-Related structure data
Related structure data | 5mgsC 5mgtC 3ff7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17108.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: lymphocytes, natural killer cell / Gene: KLRB1, CLEC5B, NKRP1A / Plasmid: pOPINGGTneo / Cell line (production host): HEK293S GnTI- / Organ (production host): Human embryonic kidney / Production host: Homo sapiens (human) / References: UniProt: Q12918 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | #5: 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: 2.32 Å3/Da / Density % sol: 47 % Description: A hexagonal crystal with dimensions 150, 150, 20 um |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 20% (w/v) PEG 3350, 200 mM di-sodium tartrate pH 7.2 PROTEIN CONCENTRATION 20 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.3 Å / Num. obs: 32555 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 39.5 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 41 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 40.5 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1900 / CC1/2: 0.975 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ff7 Resolution: 1.8→43.3 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 1.787 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 33.5 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→43.3 Å
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