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Yorodumi- PDB-1lqv: Crystal structure of the Endothelial protein C receptor with phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lqv | |||||||||
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Title | Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C. | |||||||||
Components |
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Keywords | BLOOD CLOTTING / Gla (gamma-carboxyglutamic acid) residues / phospholipid binding groove / Ca ion binding | |||||||||
Function / homology | Function and homology information protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall ...protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / negative regulation of inflammatory response / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / signaling receptor activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / focal adhesion / centrosome / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Oganesyan, V. / Oganesyan, N. / Terzyan, S. / Dongfeng, Q. / Dauter, Z. / Esmon, N.L. / Esmon, C.T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The crystal structure of the endothelial protein C receptor and a bound phospholipid. Authors: Oganesyan, V. / Oganesyan, N. / Terzyan, S. / Qu, D. / Dauter, Z. / Esmon, N.L. / Esmon, C.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lqv.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lqv.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lqv_validation.pdf.gz | 827.9 KB | Display | wwPDB validaton report |
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Full document | 1lqv_full_validation.pdf.gz | 839.1 KB | Display | |
Data in XML | 1lqv_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 1lqv_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lqv ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lqv | HTTPS FTP |
-Related 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
-Protein / Protein/peptide / Sugars , 3 types, 10 molecules ABCD
#1: Protein | Mass: 22046.562 Da / Num. of mol.: 2 / Fragment: Extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEE EPCR / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO lecI / References: UniProt: Q9UNN8 #2: Protein/peptide | Mass: 4359.409 Da / Num. of mol.: 2 / Fragment: Protein C Gla domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: Cleavage happened during crystallization and the crystal contains only the N-terminal domain (Gla domain) of protein C. References: UniProt: P04070 #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 445 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #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: 2.43 Å3/Da / Density % sol: 49.39 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: peg 400, potassium chloride, magnesium chloride, calcium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2001 / Details: mirrors |
Radiation | Monochromator: CuKa / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. all: 73694 / Num. obs: 66375 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.041 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.55→1.61 Å / % possible obs: 49.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 27 / Num. unique all: 66000 / Rsym value: 0.043 / % possible all: 91 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 98 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 83.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Endothelial protein C receptor Resolution: 1.6→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→12 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.189 |