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- EMDB-19165: Trimeric HSV-2F gB ectodomain in postfusion conformation with thr... -

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Basic information

Entry
Database: EMDB / ID: EMD-19165
TitleTrimeric HSV-2F gB ectodomain in postfusion conformation with three bound HDIT101 Fab molecules.
Map datamain map
Sample
  • Complex: Trimeric HSV-2G gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules
    • Protein or peptide: Envelope glycoprotein B
    • Protein or peptide: HDIT101 Fab heavy chain
    • Protein or peptide: HDIT101 Fab light chain
Keywordsectodomain / post-fusion / fab molecule / trimeric / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHomo sapiens (human) / Human herpesvirus 2 strain G
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsKalbermatter 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 Germany, 1 items
OrganizationGrant numberCountry
Heidelberg ImmunoTherapeutics GmbH Germany
CitationJournal: 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
DepositionDec 14, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19165.png

Downloads & links

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Map

FileDownload / File: emd_19165.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 300 pix.
= 386.614 Å		1.29 Å/pix.
x 300 pix.
= 386.614 Å		1.29 Å/pix.
x 300 pix.
= 386.614 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28871 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.06869662 - 0.12941822
Average (Standard dev.)0.00015110042 (±0.0023273404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 386.6143 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19165_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_19165_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_19165_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Trimeric HSV-2G gB ectodomain in post-fusion conformation with th...

EntireName: Trimeric HSV-2G gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules
Components
  • Complex: Trimeric HSV-2G gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules
    • Protein or peptide: Envelope glycoprotein B
    • Protein or peptide: HDIT101 Fab heavy chain
    • Protein or peptide: HDIT101 Fab light chain

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Supramolecule #1: Trimeric HSV-2G gB ectodomain in post-fusion conformation with th...

SupramoleculeName: Trimeric HSV-2G gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 523 KDa

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2 strain G
Molecular weightTheoretical: 79.378227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAPAAPRASG GVAATVAANG GPASRPPPVP SPATTRARKR KTKKPPERPE ATPPPDANAT VAAGHATLRA HLREIKVENA DAQFYVCPP PTGATVVQFE QPRRCPTRPE GQNYTEGIAV VFKENIAPYK FKATMYYKDV TVSQVWFGHR YSQFMGIFED R APVPFEEV ...String:
AAPAAPRASG GVAATVAANG GPASRPPPVP SPATTRARKR KTKKPPERPE ATPPPDANAT VAAGHATLRA HLREIKVENA DAQFYVCPP PTGATVVQFE QPRRCPTRPE GQNYTEGIAV VFKENIAPYK FKATMYYKDV TVSQVWFGHR YSQFMGIFED R APVPFEEV IDKINAKGVC RSTAKYVRNN METTAFHRDD HETDMELKPA KVATRTSRGW HTTDLKYNPS RVEAFHRYGT TV NCIVEEV DARSVYPYDE FVLATGDFVY MSPFYGYREG SHTEHTSYAA DRFKQVDGFY ARDLTTKARA TSPTTRNLLT TPK FTVAWD WVPKRPAVCT MTKWQEVDEM LRAEYGGSFR FSSDAISTTF TTNLTQYSLS RVDLGDCIGR DAREAIDRMF ARKY NATHI KVGQPQYYLA TGGFLIAYQP LLSNTLAELY VREYMREQDR KPRNATPAPL REAPSANASV ERIKTTSSIE FARLQ FTYN HIQRHVNDML GRIAVAWCEL QNHELTLWNE ARKLNPNAIA SATVGRRASA RMLGDVMAVS TCVPVAPDNV IVQNSM RVS SRPGTCYSRP LVSFRYEDQG PLIEGQLGEN NELRLTRDAL EPCTVGHRRY FIFGGGYVYF EEYAYSHQLS RADVTTV ST FIDLNITMLE DHEFVPLEVY TRHEIKDSGL LDYTEVQRRN QLHDLRFADI DTVIRADANA A

UniProtKB: Envelope glycoprotein B

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Macromolecule #2: HDIT101 Fab heavy chain

MacromoleculeName: HDIT101 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.676211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TLKESGPALV KPTQTLTLTC TFSGFSLSTS GMSVGWIRQP PGKALEWLAH IWWNNDKYYK PALKSRLTIS KDTSKNQVVL TMTNMDPVD TATYYCARIY YGYRPYAMDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
TLKESGPALV KPTQTLTLTC TFSGFSLSTS GMSVGWIRQP PGKALEWLAH IWWNNDKYYK PALKSRLTIS KDTSKNQVVL TMTNMDPVD TATYYCARIY YGYRPYAMDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT CPPCPAPELL GG PSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS VLTVLHQDWL NGK EYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP SRDELTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT TPPV LDSDG SFFLYSKLTV DKSRWQQGNV FSCSVMHEAL HNHYTQKSLS LSPGK

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Macromolecule #3: HDIT101 Fab light chain

MacromoleculeName: HDIT101 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.944691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IVMTQTPLSL PVTPGEPASI SCRSSQSIVH SNGNTYLEWY LQKPGQSPQL LIYKVSNRFS GVPDRFSGSG SGTDFTLKIS RVEAEDVGV YYCFQGSHVP WSFGQGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String:
IVMTQTPLSL PVTPGEPASI SCRSSQSIVH SNGNTYLEWY LQKPGQSPQL LIYKVSNRFS GVPDRFSGSG SGTDFTLKIS RVEAEDVGV YYCFQGSHVP WSFGQGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
50.0 mMC4H11NO3Tris
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 9700 / Average exposure time: 3.2 sec. / Average electron dose: 1.325 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Particle selectionNumber selected: 6289845
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2gum

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 234096
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2gum


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8rh1:
Trimeric HSV-2F gB ectodomain in postfusion conformation with three bound HDIT101 Fab molecules.

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