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- EMDB-46758: Cryo-EM structure of neutralizing murine antibody WS.HSV-1.24 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-46758
TitleCryo-EM structure of neutralizing murine antibody WS.HSV-1.24 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P.531E
Map data
Sample
  • Complex: WS.HSV-1.24 Fab in complex with HSV-1 gB trimer
    • Protein or peptide: Glycoprotein B
    • Protein or peptide: WS.HSV-1.24 heavy chain
    • Protein or peptide: WS.HSV-1.24 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmune complex / neutralization / herpes fusogen / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma 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
Biological speciesMus musculus (house mouse) / Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRoark RS / Shapiro LS / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Prefusion structure and neutralization of HSV-1 glycoprotein B
Authors: Roark RS / Shapiro L / Kwong PD
History
DepositionAug 27, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46758.png

Downloads & links

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Map

FileDownload / File: emd_46758.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.21415038 - 0.4403548
Average (Standard dev.)0.0030135277 (±0.012423956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46758_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_46758_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 : WS.HSV-1.24 Fab in complex with HSV-1 gB trimer

EntireName: WS.HSV-1.24 Fab in complex with HSV-1 gB trimer
Components
  • Complex: WS.HSV-1.24 Fab in complex with HSV-1 gB trimer
    • Protein or peptide: Glycoprotein B
    • Protein or peptide: WS.HSV-1.24 heavy chain
    • Protein or peptide: WS.HSV-1.24 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: WS.HSV-1.24 Fab in complex with HSV-1 gB trimer

SupramoleculeName: WS.HSV-1.24 Fab in complex with HSV-1 gB trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Glycoprotein B

MacromoleculeName: Glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 90.320102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV ...String:
MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP 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 RPVNDMLGRV AIAWCEEQNH ELTLWNEARK LNPNAIASVT VGRRVS ARM LGDVMAVSTC VPVAADNVIV QNSMRISSRP GACYSRPLVS FRYEDQGPLV EGQLGENNEL RLTRDAIEPC TVGHRRY FT FGGGYVYFEE YAYSHQLSRA DITTVSTFID LNITMLEDHE FVPLEVYTRH EIKDSGLLDY TEVQRRNQLH DLRFADID T VIHADANGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSA WSHPQFEK

UniProtKB: Glycoprotein B

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Macromolecule #2: WS.HSV-1.24 heavy chain

MacromoleculeName: WS.HSV-1.24 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.191865 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLKESGPG LVAPSQSLSI TCTVSGFSLT TYGVTWVRQP PGKGLEWLGV IWGDGSTNYH SDLISRLSIT KDNSKSQVFL KLSSLQADD TATYYCVSYY GYFDHWGQGT TLTVSSASTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP EPVTVTWNSG S LSSGVHTF ...String:
QVQLKESGPG LVAPSQSLSI TCTVSGFSLT TYGVTWVRQP PGKGLEWLGV IWGDGSTNYH SDLISRLSIT KDNSKSQVFL KLSSLQADD TATYYCVSYY GYFDHWGQGT TLTVSSASTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP EPVTVTWNSG S LSSGVHTF PAVLQSDLYT LSSSVTVPSS TWPSETVTCN VAHPASSTKV DKKIVPRDCG

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Macromolecule #3: WS.HSV-1.24 light chain

MacromoleculeName: WS.HSV-1.24 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.522848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASLGERVS LTCRASQDIG SSLNWLQQKP DGTIKRLIYA TSSLDSGVPK RFSGSRSGSD YSLTISSLES EDFVDYYCL QYASSPPTFG GGTKLEIKRT DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQSPSS LSASLGERVS LTCRASQDIG SSLNWLQQKP DGTIKRLIYA TSSLDSGVPK RFSGSRSGSD YSLTISSLES EDFVDYYCL QYASSPPTFG GGTKLEIKRT DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xrt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127859
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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