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Yorodumi- PDB-8rh0: Trimeric HSV-1F gB ectodomain in postfusion conformation with thr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rh0 | ||||||
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Title | Trimeric HSV-1F gB ectodomain in postfusion conformation with three bound HDIT102 Fab molecules. | ||||||
Components |
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Keywords | VIRAL PROTEIN / ectodomain / post-fusion / fab molecule / trimeric | ||||||
Function / homology | Function and homology information host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human alphaherpesvirus 1 (Herpes simplex virus type 1) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å | ||||||
Authors | Kalbermatter, D. / Seyfizadeh, N. / Imhof, T. / Ries, M. / Mueller, C. / Jenner, L. / Blumenschein, E. / Yendrzheyevskiy, A. / Moog, K. / Eckert, D. ...Kalbermatter, D. / Seyfizadeh, N. / Imhof, T. / Ries, M. / Mueller, C. / Jenner, L. / Blumenschein, E. / Yendrzheyevskiy, A. / Moog, K. / Eckert, D. / Engel, R. / Diebolder, P. / Chami, M. / Krauss, J. / Schaller, T. / Arndt, M. | ||||||
Funding support | 1items
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Citation | Journal: J Biomed Sci / Year: 2024 Title: Development of a highly effective combination monoclonal antibody therapy against Herpes simplex virus. Authors: Narges Seyfizadeh / David Kalbermatter / Thomas Imhof / Moritz Ries / Christian Müller / Leonie Jenner / Elisabeth Blumenschein / Alexandra Yendrzheyevskiy / Frank Grün / Kevin Moog / ...Authors: Narges Seyfizadeh / David Kalbermatter / Thomas Imhof / Moritz Ries / Christian Müller / Leonie Jenner / Elisabeth Blumenschein / Alexandra Yendrzheyevskiy / Frank Grün / Kevin Moog / Daniel Eckert / Ronja Engel / Philipp Diebolder / Mohamed Chami / Jürgen Krauss / Torsten Schaller / Michaela Arndt / Abstract: BACKGROUND: Infections with Herpes simplex virus (HSV)-1 or -2 usually present as mild chronic recurrent disease, however in rare cases can result in life-threatening conditions with a large spectrum ...BACKGROUND: Infections with Herpes simplex virus (HSV)-1 or -2 usually present as mild chronic recurrent disease, however in rare cases can result in life-threatening conditions with a large spectrum of pathology. Monoclonal antibody therapy has great potential especially to treat infections with virus resistant to standard therapies. HDIT101, a humanized IgG targeting HSV-1/2 gB was previously investigated in phase 2 clinical trials. The aim of this study was to develop a next-generation therapy by combining different antiviral monoclonal antibodies. METHODS: A lymph-node derived phage display library (LYNDAL) was screened against recombinant gB from Herpes simplex virus (HSV) -1 and HDIT102 scFv was selected for its binding characteristics using ...METHODS: A lymph-node derived phage display library (LYNDAL) was screened against recombinant gB from Herpes simplex virus (HSV) -1 and HDIT102 scFv was selected for its binding characteristics using bio-layer interferometry. HDIT102 was further developed as fully human IgG and tested alone or in combination with HDIT101, a clinically tested humanized anti-HSV IgG, in vitro and in vivo. T-cell stimulating activities by antigen-presenting cells treated with IgG-HSV immune complexes were analyzed using primary human cells. To determine the epitopes, the cryo-EM structures of HDIT101 or HDIT102 Fab bound to HSV-1F as well as HSV-2G gB protein were solved at resolutions < 3.5 Å. RESULTS: HDIT102 Fab showed strong binding to HSV-1F gB with Kd of 8.95 × 10 M and to HSV-2G gB with Kd of 3.29 × 10 M. Neutralization of cell-free virus and inhibition of cell-to-cell ...RESULTS: HDIT102 Fab showed strong binding to HSV-1F gB with Kd of 8.95 × 10 M and to HSV-2G gB with Kd of 3.29 × 10 M. Neutralization of cell-free virus and inhibition of cell-to-cell spread were comparable between HDIT101 and HDIT102. Both antibodies induced internalization of gB from the cell surface into acidic endosomes by binding distinct epitopes in domain I of gB and compete for binding. CryoEM analyses revealed the ability to form heterogenic immune complexes consisting of two HDIT102 and one HDIT101 Fab bound to one gB trimeric molecule. Both antibodies mediated antibody-dependent phagocytosis by antigen presenting cells which stimulated autologous T-cell activation. In vivo, the combination of HDIT101 and HDIT102 demonstrated synergistic effects on survival and clinical outcome in immunocompetent BALB/cOlaHsd mice. CONCLUSION: This biochemical and immunological study showcases the potential of an effective combination therapy with two monoclonal anti-gB IgGs for the treatment of HSV-1/2 induced disease conditions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rh0.cif.gz | 489.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rh0.ent.gz | 376.6 KB | Display | PDB format |
PDBx/mmJSON format | 8rh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rh0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8rh0_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8rh0_validation.xml.gz | 74.4 KB | Display | |
Data in CIF | 8rh0_validation.cif.gz | 113.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/8rh0 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/8rh0 | HTTPS FTP |
-Related structure data
Related structure data | 19164MC 8rgzC 8rh1C 8rh2C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 100449.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1) Gene: gB, UL27 / Cell line (production host): HEK293-E6 / Production host: Homo sapiens (human) / References: UniProt: P06436 #2: Antibody | Mass: 49310.387 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-E6 / Production host: Homo sapiens (human) #3: Antibody | Mass: 22403.775 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-E6 / Production host: Homo sapiens (human) |
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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 |
-Sample preparation
Component | Name: Trimeric HSV-1F gB ectodomain in post-fusion conformation with three bound HDIT102 Fab molecules Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.523 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293-E6 | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 283.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Average exposure time: 4 sec. / Electron dose: 1.15 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6611 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1059496 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208280 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2gum Accession code: 2gum / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.44→192.45 Å / Cor.coef. Fo:Fc: 0.848 / SU B: 18.753 / SU ML: 0.297 / ESU R: 0.347 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.672 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 19143 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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