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- PDB-3rkd: Hepatitis E Virus E2s domain (Genotype I) in complex with a neutr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rkd | ||||||
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Title | Hepatitis E Virus E2s domain (Genotype I) in complex with a neutralizing antibody | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Hepatitis E virus capsid protein / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() T=1 icosahedral viral capsid / host cell endoplasmic reticulum / viral capsid / host cell Golgi apparatus / host cell surface / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity ...T=1 icosahedral viral capsid / host cell endoplasmic reticulum / viral capsid / host cell Golgi apparatus / host cell surface / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, X.H. / Sivaraman, J. | ||||||
![]() | ![]() Title: Structural basis for the neutralization and genotype specificity of hepatitis E virus Authors: Tang, X.H. / Yang, C.Y. / Gu, Y. / Song, C.L. / Zhang, X. / Wang, Y.B. / Zhang, J. / Hew, C.L. / Li, S.W. / Xia, N.S. / Sivaraman, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.5 KB | Display | ![]() |
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PDB format | ![]() | 192.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.9 KB | Display | ![]() |
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Full document | ![]() | 487.4 KB | Display | |
Data in XML | ![]() | 50.3 KB | Display | |
Data in CIF | ![]() | 72.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rkcC ![]() 1qblS ![]() 3ggqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15510.313 Da / Num. of mol.: 2 / Fragment: UNP residues 459-603 / Mutation: Y532H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 23648.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Antibody | Mass: 24476.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1M HEPEPS, 0.4M KSCN, 0.4M NH4Cl, 18% PEG 3350, 5% w/v n-Dodecyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 112759 / Redundancy: 6.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GGQ and 1QBL Resolution: 1.9→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 45.6126 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.0299 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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