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- EMDB-74907: Soluble ectodomain of Herpes simplex virus 2 (HSV-2) glycoprotein... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-74907
TitleSoluble ectodomain of Herpes simplex virus 2 (HSV-2) glycoprotein B (gB) in the prefusion conformation in complex with 2c and D48 Fabs
Map data
Sample
  • Complex: HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c
    • Protein or peptide: Envelope glycoprotein B
    • Protein or peptide: Antibody D48 Heavy Chain
    • Protein or peptide: Antibody D48 Light Chain
    • Protein or peptide: Antibody 2c Heavy Chain
    • Protein or peptide: Antibody 2c Light Chain
Keywordsprefusion / ectodomain / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 2 (strain HG52) / Human herpesvirus 2 strain HG52 / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSponholtz MR / Johnson NV / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure-based design of soluble prefusion-stabilized herpes simplex virus type 2 glycoprotein B antigens
Authors: Sponholtz MR / Ma D / Byrne PO / Shu Y / Warren C / Thambi N / McCool RS / Slein MD / Johnson NV / Rose WA / Zhang L / Durr E / Wang D / McLellan JM
History
DepositionJan 1, 2026-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74907.png

Downloads & links

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Map

FileDownload / File: emd_74907.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 359.942 Å		0.83 Å/pix.
x 432 pix.
= 359.942 Å		0.83 Å/pix.
x 432 pix.
= 359.942 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.3
Minimum - Maximum-0.26240134 - 28.489588000000001
Average (Standard dev.)-0.007996564 (±0.52960324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 359.94238 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_74907_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74907_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74907_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c

EntireName: HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c
Components
  • Complex: HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c
    • Protein or peptide: Envelope glycoprotein B
    • Protein or peptide: Antibody D48 Heavy Chain
    • Protein or peptide: Antibody D48 Light Chain
    • Protein or peptide: Antibody 2c Heavy Chain
    • Protein or peptide: Antibody 2c Light Chain

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Supramolecule #1: HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c

SupramoleculeName: HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 2 (strain HG52)
Molecular weightTheoretical: 555 KDa

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1
Details: Fusion protein, homotrimer, ectodomain,Fusion protein, homotrimer, ectodomain
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2 strain HG52
Molecular weightTheoretical: 83.540695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EATPPPDANA TVAAGHATLR AHLREIKVEN ADAQFYVCPP PTGATVVQFE QPRRCPTRPE GQNYTEGIAV VFKENIAPYK FKATMYYKD VTVSQVWFGN RTSQFMGIFE DRAPVPFEEV IDKINAKGVC RSTAKYVRNN METTAFHRDD HETDMELKPA K VATRCSRG ...String:
EATPPPDANA TVAAGHATLR AHLREIKVEN ADAQFYVCPP PTGATVVQFE QPRRCPTRPE GQNYTEGIAV VFKENIAPYK FKATMYYKD VTVSQVWFGN RTSQFMGIFE DRAPVPFEEV IDKINAKGVC RSTAKYVRNN METTAFHRDD HETDMELKPA K VATRCSRG WHTTDLKYNP SRVEAFHRYG TTVNCIVEEV DARSVYPYDE FVLATGDFVY MSPFYGYREG SHTEHTSYAA DR FKQVDGF YARDLTTKAR ATSPTTRNLL TTPKFTVAWD WVPKRPAVCT MTKWQEVDEM LRAEYGGSFR FSSDAISTTF TTN LTEYSL SRVDLGDCIG RDAREAIDRM FARKYNATHI KVGQPQYYLA TGGFLIAYQP LLSNTLAELY VREYMREQDR KPRN ATPAP LREAPSANAS VERIKTTSSI EFARLQFTYN HIQRHVNDML GRIAVAWCEL QNHELTLWNE ARKLNPNAIA SATVG RRVS ARMLGDVMAV STCVPVAPDN VIVQNSMRVS SRPGTCYSRP LVSFRYEDQG PLIEGQLGEN NELRLTRDAL EPCTVG HRR YFIFGGGYVY FEEYAYSHQL SRADVTTVPP FIDLNITMLC DHEFVPLEVY TRHEIKDSGL LDYTEVQRRN QLHDLRF AD IDTVIRADAN AAMFAGGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEKGGG S GGGGSGGSAW SHPQFEK

UniProtKB: Envelope glycoprotein B

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Macromolecule #2: Antibody D48 Heavy Chain

MacromoleculeName: Antibody D48 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.402555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVETGGG VVRPGRSLRL SCTTSGFSFS GSAMHWVRQA PGKGLEWVAV ISHDGNIIQY HDSVKGRFTI SRDNSKNVLL LQMNSLRVD DTAMYYCARD VWLLPATISY AFDFWGQGTM VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVETGGG VVRPGRSLRL SCTTSGFSFS GSAMHWVRQA PGKGLEWVAV ISHDGNIIQY HDSVKGRFTI SRDNSKNVLL LQMNSLRVD DTAMYYCARD VWLLPATISY AFDFWGQGTM VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD

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Macromolecule #3: Antibody D48 Light Chain

MacromoleculeName: Antibody D48 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.476164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIWMTQSPPS LSASIGDTVT ITCRASQGIS NSIAWYQRRP GKAPELLVYA AYRLQSGVPS RLSGSGSGAE YTLTIKNMQP EDFATYYCQ QYYDNPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
VIWMTQSPPS LSASIGDTVT ITCRASQGIS NSIAWYQRRP GKAPELLVYA AYRLQSGVPS RLSGSGSGAE YTLTIKNMQP EDFATYYCQ QYYDNPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: Antibody 2c Heavy Chain

MacromoleculeName: Antibody 2c Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.262426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLKESGPG ILLPSQTLSL TCSFSGFSLS TSGMSVGWIR QPSGKGLEWL GHIWWNNDKY YKPALKSRLT ISKDTSNKQV FLKIASVVT ADTATYYCAR IYYGYRPYAM DYWGQGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVTLKESGPG ILLPSQTLSL TCSFSGFSLS TSGMSVGWIR QPSGKGLEWL GHIWWNNDKY YKPALKSRLT ISKDTSNKQV FLKIASVVT ADTATYYCAR IYYGYRPYAM DYWGQGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCD

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Macromolecule #5: Antibody 2c Light Chain

MacromoleculeName: Antibody 2c Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.022785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVLMTQTPLS LPVSLGDQAS ISCRSSQSIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PWSFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DVLMTQTPLS LPVSLGDQAS ISCRSSQSIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PWSFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ModelAngelo models
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 227517
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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