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- PDB-4dgy: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -

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Basic information

Entry
Database: PDB / ID: 4dgy
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody HCV1, C2 form
Components
  • E2 peptide
  • HCV1 Heavy Chain
  • HCV1 Light Chain
KeywordsIMMUNE 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
: / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal ...: / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsKong, L. / Wilson, I.A. / Law, M.
CitationJournal: 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
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: HCV1 Heavy Chain
L: HCV1 Light Chain
A: E2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9719
Polymers49,5313
Non-polymers4396
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-58 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.099, 63.065, 69.300
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-598-

HOH

21H-615-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide E2 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 HCV1 Heavy Chain


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)
#2: Antibody HCV1 Light Chain


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)

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Non-polymers , 3 types, 408 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAN N-TERMINAL ARG RESIDUE HAS BEEN ADDED TO THE E2 PEPTIDE TO AID SOLUBILITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GIZ

3giz


Resolution: 1.798→28.764 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 2809 5.08 %RANDOM
Rwork0.1876 ---
all0.1893 ---
obs0.1893 55268 98.05 %-
Solvent computationShrinkage 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 parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.8058 Å20 Å2-1.2544 Å2
2--6.4408 Å20 Å2
3----7.0564 Å2
Refinement stepCycle: LAST / Resolution: 1.798→28.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 26 402 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073661
X-RAY DIFFRACTIONf_angle_d1.0744978
X-RAY DIFFRACTIONf_dihedral_angle_d12.9811321
X-RAY DIFFRACTIONf_chiral_restr0.079556
X-RAY DIFFRACTIONf_plane_restr0.004641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.82940.30261170.25982138X-RAY DIFFRACTION82
1.8294-1.86270.28381650.24742654X-RAY DIFFRACTION100
1.8627-1.89850.27421270.23312681X-RAY DIFFRACTION100
1.8985-1.93720.28231510.23062659X-RAY DIFFRACTION100
1.9372-1.97930.2711430.23332674X-RAY DIFFRACTION100
1.9793-2.02540.27221440.22342632X-RAY DIFFRACTION100
2.0254-2.0760.25741380.21412661X-RAY DIFFRACTION100
2.076-2.13210.25031380.21882677X-RAY DIFFRACTION100
2.1321-2.19480.26381430.20932665X-RAY DIFFRACTION100
2.1948-2.26570.24211640.20792651X-RAY DIFFRACTION100
2.2657-2.34660.26181480.20982675X-RAY DIFFRACTION100
2.3466-2.44050.26831530.21952640X-RAY DIFFRACTION100
2.4405-2.55150.26461210.21522713X-RAY DIFFRACTION100
2.5515-2.6860.26741420.20642651X-RAY DIFFRACTION100
2.686-2.85410.21881500.18912684X-RAY DIFFRACTION100
2.8541-3.07420.2271350.18662686X-RAY DIFFRACTION100
3.0742-3.38320.22061340.17442706X-RAY DIFFRACTION100
3.3832-3.87170.18171370.1642682X-RAY DIFFRACTION99
3.8717-4.87410.15991250.14292620X-RAY DIFFRACTION96
4.8741-28.76750.19971340.19042310X-RAY DIFFRACTION83

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