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- EMDB-19163: Trimeric HSV-1F gB ectodomain in postfusion conformation with thr... -
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Open data
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Basic information
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Title | Trimeric HSV-1F gB ectodomain in postfusion conformation with three bound HDIT101 Fab molecules. | |||||||||
![]() | Main sharpened map | |||||||||
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![]() | ectodomain / post-fusion / fab molecule / trimeric / VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
![]() | 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 | 1 items
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.9 KB 21.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 66.9 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 80.9 MB 80.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rgzMC ![]() 8rh0C ![]() 8rh1C ![]() 8rh2C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Main sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2876 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: half map 1
File | emd_19163_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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-Half map: half map 2
File | emd_19163_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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Sample components
-Entire : Trimeric HSV-1F gB ectodomain in post-fusion conformation with th...
Entire | Name: Trimeric HSV-1F gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules |
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Components |
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-Supramolecule #1: Trimeric HSV-1F gB ectodomain in post-fusion conformation with th...
Supramolecule | Name: Trimeric HSV-1F gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 523 KDa |
-Macromolecule #1: Envelope glycoprotein B
Macromolecule | Name: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 100.449375 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRQGAPARGC RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPAPG PAPTGDTKPK KNKKPKNPPP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV ...String: MRQGAPARGC RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPAPG PAPTGDTKPK KNKKPKNPPP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV TVSQVWFGHR YSQFMGIFED RAPVPFEEVI DKINAKGVCR STAKYVRNNL ETTAFHRDDH ETDMELKPAN AA TRTSRGW HTTDLKYNPS RVEAFHRYGT TVNCIVEEVD ARSVYPYDEF VLATGDFVYM SPFYGYREGS HTEHTSYAAD RFK QVDGFY ARDLTTKARA TAPTTRNLLT TPKFTVAWDW VPKRPSVCTM TKWQEVDEML RSEYGGSFRF SSDAISTTFT TNLT EYPLS RVDLGDCIGK DARDAMDRIF ARRYNATHIK VGQPQYYLAN GGFLIAYQPL LSNTLAELYV REHLREQSRK PPNPT PPPP GASANASVER IKTTSSIEFA RLQFTYNHIQ RHVNDMLGRV AIAWCELQNH ELTLWNEARK LNPNAIASAT VGRRVS ARM LGDVMAVSTC VPVAADNVIV QNSMRISSRP GACYSRPLVS FRYEDQGPLV EGQLGENNEL RLTRDAIEPC TVGHRRY FT FGGGYVYFEE YAYSHQLSRA DITTVSTFID LNITMLEDHE FVPLEVYTRH EIKDSGLLDY TEVQRRNQLH DLRFADID T VIHADANAAM FAGLGAFFEG MGDLGRAVGK VVMGIVGGVV SAVSGVSSFM SNPFGALAVG LLVLAGLAAA FFAFRYVMR LQSNPMKALY PLTTKELKNP TNPDASGEGE EGGDFDEAKL AEAREMIRYM ALVSAMEHTE HKAKKKGTSA LLSAKVTDMV MRKRRNTNY TQVPNKDGDA DEDDLAA UniProtKB: Envelope glycoprotein B |
-Macromolecule #2: HDIT101 Fab heavy chain
Macromolecule | Name: HDIT101 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.676211 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: HDIT101 Fab light chain
Macromolecule | Name: HDIT101 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.944691 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5815 / Average exposure time: 4.0 sec. / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |