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Yorodumi- EMDB-19166: Trimeric HSV-2G gB ectodomain in postfusion conformation with thr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19166 | |||||||||
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Title | Trimeric HSV-2G gB ectodomain in postfusion conformation with three bound HDIT102 Fab molecules. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ectodomain / 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 | |||||||||
Biological species | Homo sapiens (human) / Human herpesvirus 2 strain G | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 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 | Germany, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19166.map.gz | 8.2 MB | EMDB map data format | |
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Header (meta data) | emd-19166-v30.xml emd-19166.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19166_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_19166.png | 66.6 KB | ||
Masks | emd_19166_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-19166.cif.gz | 7 KB | ||
Others | emd_19166_half_map_1.map.gz emd_19166_half_map_2.map.gz | 80.7 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19166 | HTTPS FTP |
-Validation report
Summary document | emd_19166_validation.pdf.gz | 705.7 KB | Display | EMDB validaton report |
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Full document | emd_19166_full_validation.pdf.gz | 705.3 KB | Display | |
Data in XML | emd_19166_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_19166_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19166 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19166 | HTTPS FTP |
-Related structure data
Related structure data | 8rh2MC 8rgzC 8rh0C 8rh1C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19166.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
File | emd_19166_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19166_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19166_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trimeric HSV-2G gB ectodomain in post-fusion conformation with th...
Entire | Name: Trimeric HSV-2G 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-2G gB ectodomain in post-fusion conformation with th...
Supramolecule | Name: Trimeric HSV-2G 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: Homo sapiens (human) |
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: Human herpesvirus 2 strain G |
Molecular weight | Theoretical: 79.378227 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: HDIT102 Fab heavy chain
Macromolecule | Name: HDIT102 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.310387 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVQSGAE VKTPGASVRV SCKASGHTFR TFDINWVRQA AGQGLEWMGW MSPNSGNTGY ARQFQGRVTM TRNISANTAY MELRGLRFD DTAVYYCARG PGSTGTTGSM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String: EVQLVQSGAE VKTPGASVRV SCKASGHTFR TFDINWVRQA AGQGLEWMGW MSPNSGNTGY ARQFQGRVTM TRNISANTAY MELRGLRFD DTAVYYCARG PGSTGTTGSM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTCPPCPAPE LL GGPSVFL FPPKPKDTLM ISRTPEVTCV VVDVSHEDPE VKFNWYVDGV EVHNAKTKPR EEQYNSTYRV VSVLTVLHQD WLN GKEYKC KVSNKALPAP IEKTISKAKG QPREPQVYTL PPSRDELTKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY KTTP PVLDS DGSFFLYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK |
-Macromolecule #3: HDIT102 Fab light chain
Macromolecule | Name: HDIT102 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.403775 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QAGLTQPPSV SVAPGKTARI SCGGNNIGSK SVHWYQQKPG QAPVLVIYYD SDRPSGIPER FSGSNSGNTA TLTISRVEAG DEADYYCQV WDSGSVVFGG GTKLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS ...String: QAGLTQPPSV SVAPGKTARI SCGGNNIGSK SVHWYQQKPG QAPVLVIYYD SDRPSGIPER FSGSNSGNTA TLTISRVEAG DEADYYCQV WDSGSVVFGG GTKLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TECS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP |
-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: 17039 / Average exposure time: 3.0 sec. / Average electron dose: 1.256 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |