+Open data
-Basic information
Entry | Database: PDB / ID: 5vmg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Influenza hemagglutinin H1 mutant DH1E in complex with 6'SLN | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / influenza / hemagglutinin / receptor | |||||||||
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 / membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Ni, F. / Kondrashkina, E. / Wang, Q. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Virology / Year: 2017 Title: Determinant of receptor-preference switch in influenza hemagglutinin. Authors: Ni, F. / Kondrashkina, E. / Wang, Q. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vmg.cif.gz | 550.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vmg.ent.gz | 460.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vmg_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5vmg_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5vmg_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 5vmg_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/5vmg ftp://data.pdbj.org/pub/pdb/validation_reports/vm/5vmg | HTTPS FTP |
-Related structure data
Related structure data | 5vmcC 5vmfC 5vmjC 2wrgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35954.332 Da / Num. of mol.: 3 / Mutation: Del133/D190E/D225G/Q226L/G228S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/New_York/1/18(H1N1)) Strain: A/New_York/1/18(H1N1) / Gene: HA / Production host: unidentified baculovirus / References: UniProt: Q9WFX4 #2: Protein | Mass: 21725.062 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Brevig Mission/1/1918 H1N1) Strain: A/Brevig Mission/1/1918 H1N1 / Gene: HA / Production host: unidentified baculovirus / References: UniProt: Q9WFX3 |
---|
-Sugars , 5 types, 8 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
---|---|---|---|---|---|---|---|
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine | #7: Sugar | |
-Non-polymers , 1 types, 746 molecules
#8: Water | ChemComp-HOH / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.77 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.20 M NaF, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.69 Å / Num. obs: 68026 / % possible obs: 100 % / Redundancy: 4.5 % / Net I/σ(I): 10.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WRG Resolution: 2.45→45.671 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 21.17 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→45.671 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|