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- PDB-2vsm: Nipah virus attachment glycoprotein in complex with human cell su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vsm | ||||||
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Title | Nipah 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 / membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / lymph vessel development / regulation of chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis ...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 / 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 / clathrin-dependent endocytosis of virus by host cell / cell adhesion / host cell surface receptor binding / focal adhesion / glutamatergic synapse / viral envelope / positive regulation of cell population proliferation / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / 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 | ![]() | 145.9 KB | Display | ![]() |
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PDB format | ![]() | 112.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.6 KB | Display | ![]() |
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Full document | ![]() | 475.5 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 46.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vskC ![]() 1nukS ![]() 1v3eS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() | ||
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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.) ![]() ![]() | ||
#3: Chemical | ChemComp-IPA / | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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