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Open data
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Basic information
Entry | Database: PDB / ID: 9ih8 | ||||||||||||||||||
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Title | HSV-2 postfusion glycoprotein B | ||||||||||||||||||
![]() | Envelope glycoprotein B | ||||||||||||||||||
![]() | VIRAL PROTEIN / Glycoprotein B / viral membrane fusion protein / Herpes simplex virus 2 / HSV-2 / gB | ||||||||||||||||||
Function / homology | ![]() host cell Golgi membrane / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.21 Å | ||||||||||||||||||
![]() | Vollmer, B. / Mulvaney, T. / Ebel, H. / Nentwig, J. / Gruenewald, K. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2. Authors: Benjamin Vollmer / Henriette Ebel / Renate Rees / Julia Nentwig / Thomas Mulvaney / Jürgen Schünemann / Jens Krull / Maya Topf / Dirk Görlich / Kay Grünewald / ![]() Abstract: The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at ...The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at least ten different glycoproteins, which are necessary for host cell tropism, attachment and entry. The best conserved among them, glycoprotein B (gB), is essential as it performs membrane fusion by undergoing extensive rearrangements from a prefusion to postfusion conformation. At present, there are no antiviral drugs targeting gB or neutralizing antibodies directed against its prefusion form, because of the difficulty in structurally determining and using this metastable conformation. Here we show the isolation of prefusion-specific nanobodies, one of which exhibits strong neutralizing and cross-species activity. By mutational stabilization we solved the herpes simplex virus 1 gB full-length prefusion structure, which allowed the bound epitope to be determined. Our analyses show the membrane-embedded regions of gB and previously unresolved structural features, including a new fusion loop arrangement, providing insights into the initial conformational changes required for membrane fusion. Binding an epitope spanning three domains, proximal only in the prefusion state, the nanobody keeps wild-type HSV-2 gB in this conformation and enabled its native prefusion structure to be determined. This also indicates the mode of neutralization and an attractive avenue for antiviral interventions. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 356.2 KB | Display | ![]() |
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PDB format | ![]() | 274.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 43.7 KB | Display | |
Data in CIF | ![]() | 63.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 52863MC ![]() 52963MC ![]() 52965MC ![]() 52966MC ![]() 9q9lC ![]() 9q9nC ![]() 9q9sC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 104648.422 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Full-length protein + 3C protease cleavage site + Strep-Tag II Source: (gene. exp.) ![]() Details (production host): Lentivirus plasmid for stable expression, CAG promotor Cell line (production host): HEK-293T / Organ (production host): Kidney / Production host: ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Has ligand of interest | N | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human herpesvirus 2 strain 333 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | |||||||||||||||||||||||||
Natural host | Organism: Homo sapiens | |||||||||||||||||||||||||
Buffer solution | pH: 7.8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: The grid was coated with carbon prior to use / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 80 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.197 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14886 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3833942 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 323536 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 38.46 / Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: ModelAngelo / Source name: Other / Type: in silico model |