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Yorodumi- PDB-6woq: Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6woq | |||||||||
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Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 1a bound to neutralizing antibody HC1AM and non neutralizing antibody E1 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/Viral Protein / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69 / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex | |||||||||
Function / homology | Function and homology information positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Hepatitis C virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.667 Å | |||||||||
Authors | Tzarum, N. / Wilson, I.A. / Law, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Adv / Year: 2020 Title: An alternate conformation of HCV E2 neutralizing face as an additional vaccine target. Authors: Tzarum, N. / Giang, E. / Kadam, R.U. / Chen, F. / Nagy, K. / Augestad, E.H. / Velazquez-Moctezuma, R. / Keck, Z.Y. / Hua, Y. / Stanfield, R.L. / Dreux, M. / Prentoe, J. / Foung, S.K.H. / ...Authors: Tzarum, N. / Giang, E. / Kadam, R.U. / Chen, F. / Nagy, K. / Augestad, E.H. / Velazquez-Moctezuma, R. / Keck, Z.Y. / Hua, Y. / Stanfield, R.L. / Dreux, M. / Prentoe, J. / Foung, S.K.H. / Bukh, J. / Wilson, I.A. / Law, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6woq.cif.gz | 390.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6woq.ent.gz | 311 KB | Display | PDB format |
PDBx/mmJSON format | 6woq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6woq_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6woq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6woq_validation.xml.gz | 67.5 KB | Display | |
Data in CIF | 6woq_validation.cif.gz | 91.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/6woq ftp://data.pdbj.org/pub/pdb/validation_reports/wo/6woq | HTTPS FTP |
-Related structure data
Related structure data | 6wo3C 6wo4C 6wo5C 6worC 6wosC 4mwfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules EF
#3: Protein | Mass: 20856.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate H) / Production host: Homo sapiens (human) / References: UniProt: P27958*PLUS |
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-Antibody , 4 types, 8 molecules ACBDJGKH
#1: Antibody | Mass: 23937.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 24304.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 24198.385 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #5: Antibody | Mass: 23578.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 2 types, 8 molecules
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Sugar | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.667→35 Å / Num. obs: 33504 / % possible obs: 84.3 % / Redundancy: 2.8 % / CC1/2: 0.83 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.667→3.76 Å / Num. unique obs: 1171 / CC1/2: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MWF Resolution: 3.667→34.662 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 293.03 Å2 / Biso mean: 123.8243 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.667→34.662 Å
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Refine LS restraints |
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LS refinement shell |
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