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- PDB-5erw: Structure of HCV E2 glycoprotein antigenic Epitope II bound to th... -

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Basic information

Entry
Database: PDB / ID: 5erw
TitleStructure of HCV E2 glycoprotein antigenic Epitope II bound to the broadly neutralizing antibody HC84-26
Components
  • Anti-HCV E2 Fab HC84-26 heavy chain
  • Anti-HCV E2 Fab HC84-26 light chain
  • HCV E2 glycoprotein Epitope II
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immune system / Complex / Hepatitis C virus / E2 glycoprotein / Epitope II / VIRAL PROTEIN-IMMUNE SYSTEM 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 / hepacivirin / TBC/RABGAPs / 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 / hepacivirin / TBC/RABGAPs / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral translational frameshifting / 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 / 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
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 core protein, chain A superfamily / : / 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 / NS3 RNA helicase, C-terminal helical domain / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsGao, M. / Mariuzza, R.
CitationJournal: To Be Published
Title: Structure of HCV E2 glycoprotein antigenic Epitope II bound to the broadly neutralizing antibody HC84-26
Authors: Gao, M. / Mariuzza, R.
History
DepositionNov 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-HCV E2 Fab HC84-26 heavy chain
B: Anti-HCV E2 Fab HC84-26 light chain
C: HCV E2 glycoprotein Epitope II


Theoretical massNumber of molelcules
Total (without water)48,0063
Polymers48,0063
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-36 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.700, 101.240, 180.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody Anti-HCV E2 Fab HC84-26 heavy chain


Mass: 23087.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli (E. coli)
#2: Antibody Anti-HCV E2 Fab HC84-26 light chain


Mass: 23381.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli (E. coli)
#3: Protein/peptide HCV E2 glycoprotein Epitope II


Mass: 1536.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: P27958*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: 15% (w/v) PEG 10,000, 0.1 M Sodium citrate/ Citric acid pH 5.5, 2% (v/v) Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 5, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→45.08 Å / Num. all: 15740 / Num. obs: 15740 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 55.97 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.097 / Rsym value: 0.083 / Net I/av σ(I): 7.059 / Net I/σ(I): 11.3 / Num. measured all: 58541
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.9-3.063.30.4542.8715721410.2770.4542.895.4
3.06-3.243.40.2672.8705320880.1640.2674.696.8
3.24-3.473.50.1684.5698020150.1020.168797.9
3.47-3.743.60.1146.5681518880.0690.1149.998.4
3.74-4.13.70.0848.5652217400.0490.08412.799.3
4.1-4.5940.06610.2641316090.0360.06616.999.5
4.59-5.294.20.06110.9607714370.0320.06118.199.6
5.29-6.484.30.05113.2524712320.0280.05117.999.6
6.48-9.174.10.03817.141129910.0210.03819.699.9
9.17-51.6843.60.0416.821655990.0280.04121.899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
PHENIX1.9_1692refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.08 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1570 10 %Random selection
Rwork0.2152 14132 --
obs0.2195 15702 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.53 Å2 / Biso mean: 47.1405 Å2 / Biso min: 23.14 Å2
Refinement stepCycle: final / Resolution: 2.9→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 0 68 3368
Biso mean---45.27 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163384
X-RAY DIFFRACTIONf_angle_d1.4874608
X-RAY DIFFRACTIONf_chiral_restr0.073523
X-RAY DIFFRACTIONf_plane_restr0.008586
X-RAY DIFFRACTIONf_dihedral_angle_d15.6611192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.99360.37931310.31161179131095
2.9936-3.10060.3191390.31081252139196
3.1006-3.22470.3181360.27971217135395
3.2247-3.37140.35341390.24971260139997
3.3714-3.54910.32471390.24641252139198
3.5491-3.77130.26691450.22621298144398
3.7713-4.06240.25941400.21841266140699
4.0624-4.47080.20511450.17581306145199
4.4708-5.1170.21741470.16431323147099
5.117-6.44390.22961490.19061344149399
6.4439-45.08540.22371600.206814351595100

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