[English] 日本語
Yorodumi- PDB-6n5d: Broadly protective antibodies directed to a subdominant influenza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n5d | ||||||
---|---|---|---|---|---|---|---|
Title | Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / influenza / antibody / complex / hemagglutinin / immunogen design / glycan / 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 / 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 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Bajic, G. / Schmidt, A.G. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Cell Host Microbe / Year: 2019 Title: Influenza Antigen Engineering Focuses Immune Responses to a Subdominant but Broadly Protective Viral Epitope. Authors: Bajic, G. / Maron, M.J. / Adachi, Y. / Onodera, T. / McCarthy, K.R. / McGee, C.E. / Sempowski, G.D. / Takahashi, Y. / Kelsoe, G. / Kuraoka, M. / Schmidt, A.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6n5d.cif.gz | 404.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6n5d.ent.gz | 329.8 KB | Display | PDB format |
PDBx/mmJSON format | 6n5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n5d_validation.pdf.gz | 491.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6n5d_full_validation.pdf.gz | 525 KB | Display | |
Data in XML | 6n5d_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 6n5d_validation.cif.gz | 98.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n5d ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n5d | HTTPS FTP |
-Related structure data
Related structure data | 6n5bSC 6n5eC 1ha0S 4hkxS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31150.033 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437 #2: Antibody | Mass: 25338.352 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Homo sapiens (human) #3: Antibody | Mass: 22919.457 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.13 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9787 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -k,-h,-l / Fraction: 0.46 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→44.369 Å / Num. obs: 49440 / % possible obs: 100 % / Redundancy: 6.437 % / Biso Wilson estimate: 51.897 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.277 / Χ2: 0.914 / Net I/σ(I): 9.22 / Num. measured all: 318259 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1HA0, 6N5B, & 4HKX Resolution: 3→44.369 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.82
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.15 Å2 / Biso mean: 55.5971 Å2 / Biso min: 26.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→44.369 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
|