[English] 日本語
![](img/lk-miru.gif)
- PDB-1v3c: Structure of the hemagglutinin-neuraminidase from human parainflu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1v3c | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III: complex with NEU5AC | |||||||||
![]() | hemagglutinin-neuraminidase glycoprotein | |||||||||
![]() | HYDROLASE / PIV3 HN / NATIVE+NEU5AC / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 207.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 162.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 64.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v2iC ![]() 1v3bSC ![]() 1v3dC ![]() 1v3eC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
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 |
---|
-Sugars , 3 types, 7 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SLB.gif)
![](data/chem/img/SLB.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Sugar | |
---|
-Non-polymers , 3 types, 840 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)
#5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.46 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
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: 2.3→8.5 Å / Num. obs: 61373 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 24.8 Å2 / Net I/σ(I): 12.28 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Redundancy: 8.8 % / Num. measured all: 539280 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 3.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PIV3 HN MONOMER FROM HEXAGONAL STRUCTURE ENTRY 1V3B Resolution: 2.3→7.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 169994.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.3363 Å2 / ksol: 0.352789 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→7.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|