+Open data
-Basic information
Entry | Database: PDB / ID: 5mgt | |||||||||
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Title | Complex of human NKR-P1 and LLT1 in deglycosylated forms | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / receptor / CTL fold / natural killer cell / receptor-ligand complex | |||||||||
Function / homology | Function and homology information regulation of natural killer cell mediated cytotoxicity / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / endoplasmic reticulum / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Blaha, J. / Skalova, T. / 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 | 5mgt.cif.gz | 187.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgt.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 5mgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mgt_validation.pdf.gz | 510.5 KB | Display | wwPDB validaton report |
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Full document | 5mgt_full_validation.pdf.gz | 517.9 KB | Display | |
Data in XML | 5mgt_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 5mgt_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgt ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgt | HTTPS FTP |
-Related structure data
Related structure data | 5mgrC 5mgsC 2bpdS 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 15692.363 Da / Num. of mol.: 2 / Mutation: H176C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER CELLS, ACTIVATED MONOCYTES, B-CELLS / Gene: CLEC2D, CLAX, LLT1, OCIL / Plasmid: pTT28 / Details (production host): pTT28 / Cell line (production host): HEK293S GnTI- / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Human embryonic kidney / References: UniProt: Q9UHP7 #2: Protein | Mass: 17108.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER CELLS, NKT CELLS, TH17 CELLS / Gene: KLRB1, CLEC5B, NKRP1A / Plasmid: pOPINGGTneo / Cell line (production host): HEK293S GnTI- / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Human embryonic kidney / References: UniProt: Q12918 |
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-Sugars , 1 types, 12 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 699 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: 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: 49.64 % Description: A tetragonal crystal with dimensions 30, 30, 80 um |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.200 M Ammonium Sulphate, 20 %w/v Polyethylene Glycol MME 5000, 0.1 M Tris pH 7.5, total protein concentration 8 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: 1.9→76.91 Å / Num. obs: 78617 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 18.5 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 18 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3 / Num. unique all: 4472 / CC1/2: 0.89 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BPD Resolution: 1.9→76.91 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 2.033 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / 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: 26 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→76.91 Å
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Refine LS restraints |
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