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- EMDB-47979: The primed conformation of herpes simplex virus type 1 (HSV-1) gl... -

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Basic information

Entry
Database: EMDB / ID: EMD-47979
TitleThe primed conformation of herpes simplex virus type 1 (HSV-1) glycoprotein B (gB) mutant H516P
Map data
Sample
  • Complex: glycoprotein B of herpes simplex virus type 1
    • Protein or peptide: Envelope glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHerpes simplex virus type I (HSV-1) / glycoprotein B (gB) / class III viral membrane fusion protein / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / receptor ligand activity / 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 alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMou Z / Wang S / Dai X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM151043 United States
CitationJournal: To Be Published
Title: The primed conformation of herpes simplex virus type 1 (HSV-1) glycoprotein B (gB) mutant H516P
Authors: Mou Z / Wang S / Dai X
History
DepositionNov 20, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47979.png

Downloads & links

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Map

FileDownload / File: emd_47979.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.183053 - 3.467296
Average (Standard dev.)0.00035887113 (±0.05385017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47979_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_47979_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 : glycoprotein B of herpes simplex virus type 1

EntireName: glycoprotein B of herpes simplex virus type 1
Components
  • Complex: glycoprotein B of herpes simplex virus type 1
    • Protein or peptide: Envelope glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: glycoprotein B of herpes simplex virus type 1

SupramoleculeName: glycoprotein B of herpes simplex virus type 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Strain: strain F
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope 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)
Strain: strain F
Molecular weightTheoretical: 99.830188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDHDGDYK DHDIDYKDDD DKAPSSPGTP GVAAATQAAN GGPATPAPPA PGAPPTGDPK PKKNKKPKPP KPPRPAGDNA TVAAGHATL REHLRDIKAE NTDANFYVCP PPTGATVVQF EQPRRCPTRP EGQNYTEGIA VVFKENIAPY KFKATMYYKD V TVSQVWFG ...String:
DYKDHDGDYK DHDIDYKDDD DKAPSSPGTP GVAAATQAAN GGPATPAPPA PGAPPTGDPK PKKNKKPKPP KPPRPAGDNA TVAAGHATL REHLRDIKAE NTDANFYVCP PPTGATVVQF EQPRRCPTRP EGQNYTEGIA VVFKENIAPY KFKATMYYKD V TVSQVWFG HRYSQFMGIF EDRAPVPFEE VIDKINAKGV CRSTAKYVRN NLETTAFHRD DHETDMELKP ANAATRTSRG WH TTDLKYN PSRVEAFHRY GTTVNCIVEE VDARSVYPYD EFVLATGDFV YMSPFYGYRE GSHTEHTSYA ADRFKQVDGF YAR DLTTKA RATAPTTRNL LTTPKFTVAW DWVPKRPSVC TMTKWQEVDE MLRSEYGGSF RFSSDAISTT FTTNLTEYPL SRVD LGDCI GKDARDAMDR IFARRYNATH IKVGQPQYYL ANGGFLIAYQ PLLSNTLAEL YVREHLREQS RKPPNPTPPP PGASA NASV ERIKTTSSIE FARLQFTYNH IQRPVNDMLG RVAIAWCELQ NHELTLWNEA RKLNPNAIAS ATVGRRVSAR MLGDVM AVS TCVPVAADNV IVQNSMRISS RPGACYSRPL VSFRYEDQGP LVEGQLGENN ELRLTRDAIE PCTVGHRRYF TFGGGYV YF EEYAYSHQLS RADITTVSTF IDLNITMLED HEFVPLEVYT RHEIKDSGLL DYTEVQRRNQ LHDLRFADID TVIHADAN A AMFAGLGAFF EGMGDLGRAV GKVVMGIVGG VVSAVSGVSS FMSNPFGALA VGLLVLAGLA AAFFAFRYVM RLQSNPMKA LYPLTTKELK NPTNPDASGE GEEGGDFDEA KLAEAREMIR YMALVSAMER TEHKAKKKGT SALLSAKVTD MVMRKRRNTN YTQVPNKDG DADEDDL

UniProtKB: Envelope glycoprotein B

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris(hydroxymethyl)aminomethane hydrochloride
0.2 mg/mLDodecyl beta D-Maltoside
0.02 mg/mLCholesteryl Hemisuccinate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 363741
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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