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Yorodumi- PDB-4dgy: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -
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-Basic information
Entry | Database: PDB / ID: 4dgy | ||||||
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Title | Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody HCV1, C2 form | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Immunoglobulin Fold / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information hepacivirin / 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 / 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 / lipid droplet / SH3 domain binding ...hepacivirin / 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 / 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 / lipid droplet / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by 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 / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Kong, L. / Wilson, I.A. / Law, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural basis of hepatitis C virus neutralization by broadly neutralizing antibody HCV1. Authors: Kong, L. / Giang, E. / Robbins, J.B. / Stanfield, R.L. / Burton, D.R. / 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 | 4dgy.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dgy.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 4dgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dgy_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 4dgy_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 4dgy_validation.xml.gz | 23 KB | Display | |
Data in CIF | 4dgy_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/4dgy ftp://data.pdbj.org/pub/pdb/validation_reports/dg/4dgy | HTTPS FTP |
-Related structure data
Related structure data | 4dgvC 3gizS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 1 types, 1 molecules A
#3: Protein/peptide | Mass: 1554.710 Da / Num. of mol.: 1 / Fragment: UNP residues 51-62 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: Q9YK84, UniProt: P26663*PLUS |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24580.699 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23395.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 408 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | AN N-TERMINAL ARG RESIDUE HAS BEEN ADDED TO THE E2 PEPTIDE TO AID SOLUBILITY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→70.198 Å / Num. all: 55279 / Num. obs: 55279 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.08 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.798→1.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 5554 / Rsym value: 0.53 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GIZ Resolution: 1.798→28.764 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 22.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.122 Å2 / ksol: 0.409 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.798→28.764 Å
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Refine LS restraints |
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LS refinement shell |
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