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- PDB-1usx: Crystal structure of the Newcastle disease virus hemagglutinin-ne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1usx | ||||||||||||
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Title | Crystal structure of the Newcastle disease virus hemagglutinin-neuraminidase complexed with thiosialoside | ||||||||||||
![]() | HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN | ||||||||||||
![]() | HYDROLASE / NEURAMINIDASE / HEMAGGLUTININ / SIALIDASE | ||||||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Zaitsev, V. / Itzstein, M. / Groves, D. / Kiefel, M. / Takimoto, T. / Portner, A. / Taylor, G. | ||||||||||||
![]() | ![]() Title: Second Sialic Acid Binding Site in Newcastle Disease Virus Hemagglutinin-Neuraminidase: Implications for Fusion Authors: Zaitsev, V. / Von Itzstein, M. / Groves, D. / Kiefel, M. / Takimoto, T. / Portner, A. / Taylor, G. #1: ![]() Title: Crystal Structure of the Multifunctional Paramyxovirus Hemagglutinin-Neuraminidase Authors: Crennell, S. / Takimoto, T. / Portner, A. / Taylor, G. #2: Journal: Virology / Year: 2000 Title: Crystallization of Newcastle Disease Virus Hemagglutinin-Neuraminidase Glycoprotein Authors: Takimoto, T. / Taylor, G.L. / Crennell, S.J. / Scroggs, R.A. / Portner, A. | ||||||||||||
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 | ![]() | 265.1 KB | Display | ![]() |
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PDB format | ![]() | 214.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.2 KB | Display | ![]() |
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Full document | ![]() | 815.9 KB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1usrC ![]() 1e8vS 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: (Code: given Matrix: (0.70224, 0.7046, 0.10202), Vector: |
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Components
#1: Protein | Mass: 49856.910 Da / Num. of mol.: 3 / Fragment: HEAD DOMAIN, RESIDUES 124-577 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Polysaccharide | Type: oligosaccharide / Mass: 501.503 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.3 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 2003 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 43065 / % possible obs: 81.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 71.5 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 39099 / % possible obs: 90.4 % / Num. measured all: 454555 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 88.4 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E8V Resolution: 2.7→12 Å / Data cutoff high absF: 1000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.8 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→12 Å
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Refine LS restraints |
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