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- EMDB-37203: Cryo-EM structure of HSV-1 gB with D48 Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37203
TitleCryo-EM structure of HSV-1 gB with D48 Fab complex
Map data
Sample
  • Complex: Cryo-EM structure of HSV-1 gB with D48 Fab complex
    • Protein or peptide: D48 heavy chain
    • Protein or peptide: D48 light chain
    • Protein or peptide: Envelope glycoprotein B
KeywordsHSV-1 gB / fab / neutralizing antibody / complex / Cryo-EM / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / identical protein binding
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 1 (strain KOS)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsYang J / Sun C / Fang X / Zeng M / Liu Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82070329 China
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: hlife / Year: 2023
Title: The structure of HSV-1 gB bound to a potent neutralizing antibody reveals a conservative antigenic domain across herpesviruses
Authors: Sun C / Yang JW / Xie C / Fang XY / Bu GL / Zhao GX / Dai DL / Liu Z / Zeng MS
History
DepositionAug 15, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37203.png

Downloads & links

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Map

FileDownload / File: emd_37203.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.827 Å
Density
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.20085397 - 0.43246728
Average (Standard dev.)0.00009981576 (±0.011389267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37203_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_37203_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 : Cryo-EM structure of HSV-1 gB with D48 Fab complex

EntireName: Cryo-EM structure of HSV-1 gB with D48 Fab complex
Components
  • Complex: Cryo-EM structure of HSV-1 gB with D48 Fab complex
    • Protein or peptide: D48 heavy chain
    • Protein or peptide: D48 light chain
    • Protein or peptide: Envelope glycoprotein B

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Supramolecule #1: Cryo-EM structure of HSV-1 gB with D48 Fab complex

SupramoleculeName: Cryo-EM structure of HSV-1 gB with D48 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: D48 heavy chain

MacromoleculeName: D48 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.742861 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 DKRVGSHHHH HH

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Macromolecule #2: D48 light chain

MacromoleculeName: D48 light chain / type: protein_or_peptide / ID: 2 / 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 #3: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 (strain KOS)
Molecular weightTheoretical: 70.337844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ANFYVCPPPT GATVVQFEQP RRCPTRPEGQ NYTEGIAVVF KENIAPYKFK ATMYYKDVTV SQVWFGHRYS QFMGIFEDRA PVPFEEVID KINAKGVCRS TAKYVRNNLE TTAFHRDDHE TDMELKPANA ATRTSRGWHT TDLKYNPSRV EAFHRYGTTV N CIVEEVDA ...String:
ANFYVCPPPT GATVVQFEQP RRCPTRPEGQ NYTEGIAVVF KENIAPYKFK ATMYYKDVTV SQVWFGHRYS QFMGIFEDRA PVPFEEVID KINAKGVCRS TAKYVRNNLE TTAFHRDDHE TDMELKPANA ATRTSRGWHT TDLKYNPSRV EAFHRYGTTV N CIVEEVDA RSVYPYDEFV LATGDFVYMS PFYGYREGSH TEHTTYAADR FKQVDGFYAR DLTTKARATA PTTRNLLTTP KF TVAWDWV PKRPSVCTMT KWQEVDEMLR SEYGGSFRFS SDAISTTFTT NLTEYPLSRV DLGDCIGKDA RDAMDRIFAR RYN ATHIKV GQPQYYQANG GFLIAYQPLL SNTLAELYVR EHLREQSRKP PNPTPPPPGA SANASVERIK TTSSIEFARL QFTY NHIQR HVNDMLGRVA IAWCELQNHE LTLWNEARKL NPNAIASVTV GRRVSARMLG DVMAVSTCVP VAADNVIVQN SMRIS SRPG ACYSRPLVSF RYEDQGPLVE GQLGENNELR LTRDAIEPCT VGHRRYFTFG GGYVYFEEYA YSHQLSRADI TTVSTF IDL NITMLEDHEF VPLEVYTRHE IKDSGLLDYT EVQRRNQLHD LRFADIDTVI HA

UniProtKB: Envelope glycoprotein B

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.56 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168888
FSC plot (resolution estimation)

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