[English] 日本語
Yorodumi- PDB-6a4k: Human antibody 32D6 Fab in complex with H1N1 influenza A virus HA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a4k | ||||||
---|---|---|---|---|---|---|---|
Title | Human antibody 32D6 Fab in complex with H1N1 influenza A virus HA1 | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / antibody Fab / influenza hemagglutinin / complex structure / specific binding / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 | Influenza A virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Lee, C.C. / Ko, T.P. / Lin, L.L. / Wang, A.H.J. | ||||||
Funding support | Taiwan, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: An Effective Neutralizing Antibody Against Influenza Virus H1N1 from Human B Cells. Authors: Lee, C.C. / Yang, C.Y. / Lin, L.L. / Ko, T.P. / Chang, A.H. / Chang, S.S. / Wang, A.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6a4k.cif.gz | 516.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6a4k.ent.gz | 422.6 KB | Display | PDB format |
PDBx/mmJSON format | 6a4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a4k_validation.pdf.gz | 564.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6a4k_full_validation.pdf.gz | 603.6 KB | Display | |
Data in XML | 6a4k_validation.xml.gz | 91.4 KB | Display | |
Data in CIF | 6a4k_validation.cif.gz | 126.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a4k ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a4k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Antibody , 2 types, 8 molecules HIJKLMNO
#2: Antibody | Mass: 25556.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) #3: Antibody | Mass: 23007.432 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
---|
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 26408.572 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/California/7/2009(H1N1)) Production host: Homo sapiens (human) / References: UniProt: C3W5X2*PLUS #4: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 3 types, 202 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | AUTHORS STATE THAT THE EUROPEAN NUCLEOTIDE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.82 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14%(w/v) PEG 8000, 160mM Calcium acetate, 20%(v/v) glycerol, 80mM Sodium Cacodylate, Hydrochloric acid |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2017 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→20 Å / Num. obs: 79824 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.15→3.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7965 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GBN, 3N9G Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 17.413 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.545 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.15→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|