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Yorodumi- PDB-2vsm: Nipah virus attachment glycoprotein in complex with human cell su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vsm | ||||||
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Title | Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2 | ||||||
Components |
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Keywords | HYDROLASE / DEVELOPMENTAL PROTEIN / HENIPAVIRUS / NEUROGENESIS / GLYCOPROTEIN / PARAMYXOVIRUS / ENVELOPE PROTEIN / CELL SURFACE RECEPTOR / HENDRA / VIRION / EPHRIN / COMPLEX / MEMBRANE / B2 / EFN / NIV / EPH / HEV / HEV-G / NIPAH / VIRUS / NIV-G / PHOSPHOPROTEIN / DIFFERENTIATION / VIRAL ATTACHMENT / SIGNAL-ANCHOR / HEMAGGLUTININ / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / lymph vessel development / regulation of chemotaxis / cell migration involved in sprouting angiogenesis / regulation of postsynaptic neurotransmitter receptor internalization ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / lymph vessel development / regulation of chemotaxis / cell migration involved in sprouting angiogenesis / regulation of postsynaptic neurotransmitter receptor internalization / adherens junction organization / EPH-Ephrin signaling / Ephrin signaling / blood vessel morphogenesis / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / EPHB-mediated forward signaling / T cell costimulation / ephrin receptor binding / axon guidance / animal organ morphogenesis / postsynaptic density membrane / adherens junction / Schaffer collateral - CA1 synapse / virus receptor activity / cell-cell signaling / negative regulation of neuron projection development / presynaptic membrane / clathrin-dependent endocytosis of virus by host cell / cell adhesion / host cell surface receptor binding / focal adhesion / viral envelope / glutamatergic synapse / positive regulation of cell population proliferation / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Nipah virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bowden, T.A. / Aricescu, A.R. / Gilbert, R.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural Basis of Nipah and Hendra Virus Attachment to Their Cell-Surface Receptor Ephrin-B2 Authors: Bowden, T.A. / Aricescu, A.R. / Gilbert, R.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vsm.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vsm.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vsm ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vsm | HTTPS FTP |
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-Related structure data
Related structure data | 2vskC 1nukS 1v3eS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 46839.293 Da / Num. of mol.: 1 Fragment: B-PROPELLER, EPHRIN BINDING DOMAIN, RESIDUES 188-602 Source method: isolated from a genetically manipulated source Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN / Source: (gene. exp.) Nipah virus / Description: SYNTHETICALLY OPTIMIZED CDNA (GENEART) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9IH62, exo-alpha-sialidase | ||
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#2: Protein | Mass: 16049.366 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 28-165 Source method: isolated from a genetically manipulated source Details: N-ACETYLGLUCOSAMINE LINKAGE OBSERVED IN / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799 | ||
#3: Chemical | ChemComp-IPA / | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 18% ISOPROPANOL, 18% PEG 3350 AND 0.1 M TRI-CITRATE BUFFER PH 5.6 |
-Data collection
Diffraction | Mean temperature: 77.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 17, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 55159 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NUK AND 1V3E Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.237 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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