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- PDB-8tzy: CryoEM structure of non-neutralizing bivalent antibody CBH-4B in ... -

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Basic information

Entry
Database: PDB / ID: 8tzy
TitleCryoEM structure of non-neutralizing bivalent antibody CBH-4B in complex with Hepatitis C virus envelope glycoprotein E2
Components
  • CBH4B Heavy chain
  • CBH4B Light chain
  • envelope glycoprotein E2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HCV / E2 / Fab / antiviral / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / host cell nucleus / apoptotic process / structural molecule activity ...host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / host cell nucleus / apoptotic process / structural molecule activity / virion membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShahid, S. / Liqun, J. / Liu, Y. / Hasan, S.S. / Mariuzza, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI168048 United States
CitationJournal: To Be Published
Title: CryoEM structure of non-neutralizing bivalent antibody CBH-4B in complex with Hepatitis C virus envelope glycoprotein E2
Authors: Shahid, S. / Liqun, J. / Liu, Y. / Hasan, S.S. / Mariuzza, R.A.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBH4B Heavy chain
B: CBH4B Light chain
C: envelope glycoprotein E2
D: CBH4B Heavy chain
E: CBH4B Light chain


Theoretical massNumber of molelcules
Total (without water)137,2395
Polymers137,2395
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody CBH4B Heavy chain


Mass: 27116.373 Da / Num. of mol.: 2 / Mutation: SSAS deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CBH4B Light chain


Mass: 25359.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein envelope glycoprotein E2


Mass: 32287.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate 1) / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE18
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HCV E2-CBH-4B complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.24 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl, pH 8.0, 100 mM NaCl
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7168
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200762 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037290
ELECTRON MICROSCOPYf_angle_d0.599948
ELECTRON MICROSCOPYf_dihedral_angle_d4.5171034
ELECTRON MICROSCOPYf_chiral_restr0.0451126
ELECTRON MICROSCOPYf_plane_restr0.0041286

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