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Yorodumi- PDB-2vsk: Hendra virus attachment glycoprotein in complex with human cell s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vsk | ||||||
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Title | Hendra 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 / 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 ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / 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 / postsynaptic density membrane / animal organ morphogenesis / adherens junction / Schaffer collateral - CA1 synapse / negative regulation of neuron projection development / virus receptor activity / cell-cell signaling / host cell surface / host cell surface receptor binding / cell adhesion / symbiont entry into host cell / focal adhesion / viral envelope / glutamatergic synapse / positive regulation of cell population proliferation / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Hendra virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 | 2vsk.cif.gz | 410.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vsk.ent.gz | 339.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vsk ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vsk | HTTPS FTP |
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-Related structure data
Related structure data | 2vsmSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 46780.117 Da / Num. of mol.: 2 Fragment: B-PROPELLER, EPHRIN BINDING DOMAIN, RESIDUES 188-603 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hendra virus / Description: SYNTHETICALLY OPTIMIZED CDNA (GENEART) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O89343, exo-alpha-sialidase #2: Protein | Mass: 15773.072 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 28-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799 |
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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 25% PEG 3350 0.1 M BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 77.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 13, 2006 / Details: MIRRORS |
Radiation | Monochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 17229 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 29.75 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 82.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VSM, NIV-G-EFNB2 Resolution: 3.3→20 Å / SU ML: 0.7181 / Phase error: 34.349 / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 5.99 Å2 / ksol: 0.27 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.32 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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