[English] 日本語
Yorodumi- PDB-6n5b: Broadly protective antibodies directed to a subdominant influenza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n5b | ||||||
---|---|---|---|---|---|---|---|
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 | Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta / 2-acetamido-2-deoxy-beta-D-galactopyranose Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å | ||||||
Authors | Bajic, G. / Maron, M.J. / 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 | 6n5b.cif.gz | 267.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6n5b.ent.gz | 220.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n5b_validation.pdf.gz | 468.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6n5b_full_validation.pdf.gz | 485.6 KB | Display | |
Data in XML | 6n5b_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 6n5b_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n5b ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n5b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24139.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
---|---|
#2: Antibody | Mass: 22637.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#3: Protein | Mass: 24692.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) |
#4: Sugar | ChemComp-NGA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 12% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→46.124 Å / Num. obs: 10398 / % possible obs: 98.8 % / Redundancy: 5.158 % / Biso Wilson estimate: 114.572 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.174 / Χ2: 1.025 / Net I/σ(I): 6.1 / Num. measured all: 83144 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.5→46.124 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.63
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 274.04 Å2 / Biso mean: 134.9668 Å2 / Biso min: 82.11 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→46.124 Å
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 207.0924 Å / Origin y: 208.4011 Å / Origin z: 0.0458 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|