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- PDB-2vsk: Hendra virus attachment glycoprotein in complex with human cell s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vsk | ||||||
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Title | Hendra virus attachment glycoprotein in complex with human cell surface receptor ephrinB2 | ||||||
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![]() | 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 | ![]() 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 / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / 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 / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / adherens junction organization / EPH-Ephrin signaling / blood vessel morphogenesis / Ephrin signaling / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of keratinocyte proliferation / anatomical structure morphogenesis / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / adherens junction / animal organ morphogenesis / postsynaptic density membrane / axon guidance / Schaffer collateral - CA1 synapse / cell-cell signaling / negative regulation of neuron projection development / presynaptic membrane / virus receptor activity / host cell surface / cell adhesion / host cell surface receptor binding / symbiont entry into host cell / focal adhesion / glutamatergic synapse / viral envelope / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bowden, T.A. / Aricescu, A.R. / Gilbert, R.J. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410.8 KB | Display | ![]() |
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PDB format | ![]() | 339.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.1 KB | Display | ![]() |
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Full document | ![]() | 527.2 KB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vsmSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() #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.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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