+Open data
-Basic information
Entry | Database: PDB / ID: 2vwd | ||||||
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Title | Nipah Virus Attachment Glycoprotein | ||||||
Components | HEMAGGLUTININ-NEURAMINIDASE | ||||||
Keywords | HYDROLASE / TRANSMEMBRANE / VIRAL ATTACHMENT / ENVELOPE PROTEIN / PARAMYXOVIRUS / SIGNAL-ANCHOR / HEMAGGLUTININ / NIV / HEV / NIPAH / HEV-G / VIRUS / NIV-G / HENDRA / VIRION / MEMBRANE / HENIPAVIRUS / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Nipah virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Bowden, T.A. / Crispin, M. / Harvey, D.J. / Aricescu, A.R. / Grimes, J.M. / Jones, E.Y. / Stuart, D.I. | ||||||
Citation | Journal: J.Virol. / Year: 2008 Title: Crystal Structure and Carbohydrate Analysis of Nipah Virus Attachment Glycoprotein: A Template for Antiviral and Vaccine Design. Authors: Bowden, T.A. / Crispin, M. / Harvey, D.J. / Aricescu, A.R. / 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 | 2vwd.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vwd.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwd ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwd | HTTPS FTP |
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-Related structure data
Related structure data | 2vsmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 47196.676 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 183-602 Source method: isolated from a genetically manipulated source 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 #2: Chemical | ChemComp-GBL / #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | N-ACETYL-D-GLUCOSAMIN | |
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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 6 Details: 20% (V/V) PEG 6000, 0.1 M MES PH 6.0, 0.1 M LICL AND 0.1 M GAMMA-BUTYLACTONE 18% |
-Data collection
Diffraction | Mean temperature: 77.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. obs: 45810 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VSM Resolution: 2.25→39.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.41 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.207 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.94 Å
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Refine LS restraints |
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