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- PDB-1v3d: Structure of the hemagglutinin-neuraminidase from human parainflu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v3d | |||||||||
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Title | Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III: complex with NEU5AC2EN | |||||||||
![]() | hemagglutinin-neuraminidase glycoprotein | |||||||||
![]() | HYDROLASE / PIV3 HN / NATIVE+NEU5AC2EN / HEXAGONAL | |||||||||
Function / homology | ![]() exo-alpha-sialidase activity / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lawrence, M.C. / Borg, N.A. / Streltsov, V.A. / Pilling, P.A. / Epa, V.C. / Varghese, J.N. / McKimm-Breschkin, J.L. / Colman, P.M. | |||||||||
![]() | ![]() Title: Structure of the Haemagglutinin-neuraminidase from Human Parainfluenza Virus Type III Authors: Lawrence, M.C. / Borg, N.A. / Streltsov, V.A. / Pilling, P.A. / Epa, V.C. / Varghese, J.N. / McKimm-Breschkin, J.L. / Colman, P.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.6 KB | Display | ![]() |
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PDB format | ![]() | 161.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 65.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v2iC ![]() 1v3bSC ![]() 1v3cC ![]() 1v3eC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48107.715 Da / Num. of mol.: 2 / Fragment: RESIDUES 142-572 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: GenBank: 37958139, UniProt: Q6WJ03*PLUS, exo-alpha-sialidase |
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-Sugars , 3 types, 8 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/DAN.gif)
![](data/chem/img/DAN.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #6: Sugar | |
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-Non-polymers , 3 types, 721 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.09 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AMMONIUM AND LITHIUM PHOSPHATE, HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→190 Å / Num. obs: 58597 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 32.6 Å2 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1 / % possible all: 65.1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Redundancy: 2.7 % / Num. measured all: 155158 |
Reflection shell | *PLUS % possible obs: 65 % / Mean I/σ(I) obs: 7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PIV3 HN MONOMER FROM HEXAGONAL STRUCTURE ENTRY 1V3B Resolution: 2.28→41.39 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 353924.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 84.8512 Å2 / ksol: 0.417972 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→41.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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