[English] 日本語
Yorodumi- PDB-6bkb: Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bkb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3A | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69 | |||||||||
Function / homology | Function and homology information host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / immunoglobulin complex, circulating / immunoglobulin receptor binding / 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 ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / immunoglobulin complex, circulating / immunoglobulin receptor binding / 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / complement activation, classical pathway / antigen binding / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / blood microparticle / 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 / ribonucleoprotein complex / induction by virus of host autophagy / immune response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / extracellular space / RNA binding / extracellular exosome / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Recombinant Hepatitis C virus HK6a/JFH-1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å | |||||||||
Authors | Tzarum, N. / Wilson, I.A. / Law, M. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Sci Adv / Year: 2019 Title: Genetic and structural insights into broad neutralization of hepatitis C virus by human VH1-69 antibodies. Authors: Tzarum, N. / Giang, E. / Kong, L. / He, L. / Prentoe, J. / Augestad, E. / Hua, Y. / Castillo, S. / Lauer, G.M. / Bukh, J. / Zhu, J. / Wilson, I.A. / Law, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6bkb.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6bkb.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bkb ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bkb | HTTPS FTP |
---|
-Related structure data
Related structure data | 6bkcC 6bkdC 4mwfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24581.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 |
---|---|
#3: Antibody | Mass: 23296.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6PIL8 |
-Protein / Non-polymers , 2 types, 16 molecules E
#2: Protein | Mass: 20707.395 Da / Num. of mol.: 1 / Mutation: N448D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Recombinant Hepatitis C virus HK6a/JFH-1 Production host: Homo sapiens (human) / References: UniProt: B9V0E2 |
---|---|
#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 4 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
---|---|
#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 20% (w/v) PEG 3500, 0.2M sodium-citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.598→50 Å / Num. obs: 26290 / % possible obs: 91.7 % / Redundancy: 10.9 % / Rpim(I) all: 0.03 / Rsym value: 0.12 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 998 / CC1/2: 0.68 / % possible all: 46.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4mwf Resolution: 2.799→33.382 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29 / 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: 2.799→33.382 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|