[English] 日本語
Yorodumi- PDB-5wko: Crystal structure of antibody 27F3 recognizing the HA from A/Cali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wko | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus | ||||||
Components |
| ||||||
Keywords | ANTIVIRAL PROTEIN / 27F3 H1 HA A/California/04/2009 | ||||||
Function / homology | Function and homology information immunoglobulin complex / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 ...immunoglobulin complex / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.492 Å | ||||||
Authors | Wilson, A. / Lang, S. / Zhu, X. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Cell Rep / Year: 2017 Title: Antibody 27F3 Broadly Targets Influenza A Group 1 and 2 Hemagglutinins through a Further Variation in VH1-69 Antibody Orientation on the HA Stem. Authors: Lang, S. / Xie, J. / Zhu, X. / Wu, N.C. / Lerner, R.A. / Wilson, I.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wko.cif.gz | 2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wko.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 5wko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wko ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wko | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23817.703 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Production host: Homo sapiens (human) / References: UniProt: Q6N089 #2: Antibody | Mass: 23140.697 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q9UL78, UniProt: Q6P5S8 #3: Protein | Mass: 36729.402 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: HA / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C3W5S1 #4: Protein | Mass: 20206.320 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A023ZYH9, UniProt: C5MVT7*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.72 Å3/Da / Density % sol: 78.51 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 |
-Data collection
Diffraction | Mean temperature: 77.2 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 177944 / % possible obs: 97 % / Redundancy: 5.7 % / CC1/2: 0.97 / Rpim(I) all: 0.08 / Rsym value: 0.13 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8765 / CC1/2: 0.73 / Rpim(I) all: 0.45 / Rsym value: 0.76 / % possible all: 94.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M4Y 4FQH 4FQL Resolution: 3.492→49.451 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / 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: 3.492→49.451 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 98.7608 Å / Origin y: 0.2239 Å / Origin z: 46.8985 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |