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- PDB-4n0y: Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic r... -

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Basic information

Entry
Database: PDB / ID: 4n0y
TitleStructure of the Hepatitis C Envelope Glycoprotein E1 antigenic region 314-324 bound to the cross-neutralizing antibody IGH526
Components
  • HCV E1 peptide
  • IGH526 Heavy Chain
  • IGH526 Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin Fold / Amidated c-terminus
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 / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / Toll-like receptor 2 binding / : / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / 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 / lipid droplet / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / ribonucleoprotein complex / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / extracellular region / ATP binding / nucleus / plasma 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 non-structural protein NS4b ...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 / helicase superfamily c-terminal 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Capsid protein C
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å
AuthorsKong, L. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure of Hepatitis C Virus Envelope Glycoprotein E1 Antigenic Site 314-324 in Complex with Antibody IGH526.
Authors: Kong, L. / Kadam, R.U. / Giang, E. / Ruwona, T.B. / Nieusma, T. / Culhane, J.C. / Stanfield, R.L. / Dawson, P.E. / Wilson, I.A. / Law, M.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: IGH526 Heavy Chain
L: IGH526 Light Chain
A: HCV E1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,46211
Polymers48,7823
Non-polymers6808
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-43 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.326, 67.628, 120.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide HCV E1 peptide


Mass: 1366.678 Da / Num. of mol.: 1 / Fragment: antigenic site (UNP residues 314-324) / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: R9TE34, UniProt: P27958*PLUS

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Antibody , 2 types, 2 molecules HL

#1: Antibody IGH526 Heavy Chain


Mass: 24567.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody IGH526 Light Chain


Mass: 22848.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 348 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% (w/v) PEG 6000, 1M lithium chloride and 0.1 M citric acid, pH 4.0, 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: Jul 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→30.67 Å / Num. obs: 55627 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.75→1.78 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.749→30.664 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2818 5.07 %RANDOM
Rwork0.179 ---
obs0.1805 55547 99.89 %-
all-55547 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.749→30.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 43 340 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093510
X-RAY DIFFRACTIONf_angle_d1.274779
X-RAY DIFFRACTIONf_dihedral_angle_d12.7511243
X-RAY DIFFRACTIONf_chiral_restr0.087536
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7488-1.7790.26021410.24942550X-RAY DIFFRACTION98
1.779-1.81130.27681510.24652568X-RAY DIFFRACTION100
1.8113-1.84620.2611430.22552618X-RAY DIFFRACTION100
1.8462-1.88380.26471590.21332583X-RAY DIFFRACTION100
1.8838-1.92480.23661260.19912604X-RAY DIFFRACTION100
1.9248-1.96960.23641250.19322652X-RAY DIFFRACTION100
1.9696-2.01880.21461510.19132585X-RAY DIFFRACTION100
2.0188-2.07340.22721290.17962634X-RAY DIFFRACTION100
2.0734-2.13440.21691220.18362624X-RAY DIFFRACTION100
2.1344-2.20320.19241480.18392611X-RAY DIFFRACTION100
2.2032-2.2820.22241480.18682607X-RAY DIFFRACTION100
2.282-2.37330.25681340.19252642X-RAY DIFFRACTION100
2.3733-2.48130.25971380.18982615X-RAY DIFFRACTION100
2.4813-2.6120.21071540.19442638X-RAY DIFFRACTION100
2.612-2.77560.21461600.18972616X-RAY DIFFRACTION100
2.7756-2.98970.21311300.18452672X-RAY DIFFRACTION100
2.9897-3.29030.21141660.17112639X-RAY DIFFRACTION100
3.2903-3.76560.17941300.16182695X-RAY DIFFRACTION100
3.7656-4.74150.1761330.14232731X-RAY DIFFRACTION100
4.7415-30.66820.19621300.18542845X-RAY DIFFRACTION100

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