[English] 日本語
Yorodumi- PDB-6iut: Crystal structure of influenza A virus H5 hemagglutinin globular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iut | |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody AVFluIgG01 | |||||||||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||||||||
Keywords | IMMUNE SYSTEM / influenza virus / HPAI / H5N1 / neutralizing antibody / epitope / major vulnerable site / vaccine development | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) Influenza A virus | |||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||||||||||||||||||||||||||
Authors | Wang, P. / Zuo, Y. / Sun, J. / Zhang, L. / Wang, X. | |||||||||||||||||||||||||||||||||
Funding support | China, 10items
| |||||||||||||||||||||||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2019 Title: Structural and functional definition of a vulnerable site on the hemagglutinin of highly pathogenic avian influenza A virus H5N1. Authors: Wang, P. / Zuo, Y. / Sun, J. / Zuo, T. / Zhang, S. / Guo, S. / Shi, X. / Liang, M. / Zhou, P. / Zhang, L. / Wang, X. | |||||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6iut.cif.gz | 145.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iut.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 6iut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iut_validation.pdf.gz | 835 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6iut_full_validation.pdf.gz | 849.9 KB | Display | |
Data in XML | 6iut_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 6iut_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/6iut ftp://data.pdbj.org/pub/pdb/validation_reports/iu/6iut | HTTPS FTP |
-Related structure data
Related structure data | 6iuvC 5dutS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23132.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
---|---|
#2: Antibody | Mass: 23300.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
-Protein / Non-polymers , 2 types, 152 molecules A
#3: Protein | Mass: 26252.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Anhui/1/2005(H5N1)) Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1WDM0 |
---|---|
#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.31 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 25% w/v Polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39949 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.957 / Num. unique obs: 3508 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DUT Resolution: 2.3→42.066 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.08
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→42.066 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|