[English] 日本語
Yorodumi
- EMDB-52863: HSV-2 postfusion glycoprotein B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52863
TitleHSV-2 postfusion glycoprotein B
Map dataPostfusion conformation structure of the Herpes Simplex Virus 2 glycoprotein B
Sample
  • Virus: Human herpesvirus 2 strain 333
    • Protein or peptide: Envelope glycoprotein B
KeywordsGlycoprotein B / viral membrane fusion protein / Herpes simplex virus 2 / HSV-2 / gB / VIRAL PROTEIN
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 333
Methodsingle particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsVollmer B / Mulvaney T / Ebel H / Nentwig J / Gruenewald K
Funding support Germany, United Kingdom, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 152/772-1 Germany
German Research Foundation (DFG)152/774-1 Germany
German Research Foundation (DFG)152/776-1 Germany
German Federal Ministry for Education and ResearchASPIRE project Germany
Wellcome Trust209250/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2025
Title: A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2.
Authors: Benjamin Vollmer / Henriette Ebel / Renate Rees / Julia Nentwig / Thomas Mulvaney / Jürgen Schünemann / Jens Krull / Maya Topf / Dirk Görlich / Kay Grünewald /
Abstract: The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at ...The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at least ten different glycoproteins, which are necessary for host cell tropism, attachment and entry. The best conserved among them, glycoprotein B (gB), is essential as it performs membrane fusion by undergoing extensive rearrangements from a prefusion to postfusion conformation. At present, there are no antiviral drugs targeting gB or neutralizing antibodies directed against its prefusion form, because of the difficulty in structurally determining and using this metastable conformation. Here we show the isolation of prefusion-specific nanobodies, one of which exhibits strong neutralizing and cross-species activity. By mutational stabilization we solved the herpes simplex virus 1 gB full-length prefusion structure, which allowed the bound epitope to be determined. Our analyses show the membrane-embedded regions of gB and previously unresolved structural features, including a new fusion loop arrangement, providing insights into the initial conformational changes required for membrane fusion. Binding an epitope spanning three domains, proximal only in the prefusion state, the nanobody keeps wild-type HSV-2 gB in this conformation and enabled its native prefusion structure to be determined. This also indicates the mode of neutralization and an attractive avenue for antiviral interventions.
History
DepositionFeb 20, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52863.png

Downloads & links

-
Map

FileDownload / File: emd_52863.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostfusion conformation structure of the Herpes Simplex Virus 2 glycoprotein B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 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: 0.102
Minimum - Maximum-0.29370964 - 0.8253066
Average (Standard dev.)-0.00044339354 (±0.016465489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Postfusion conformation structure of the Herpes Simplex Virus...

Fileemd_52863_additional_1.map
AnnotationPostfusion conformation structure of the Herpes Simplex Virus 2 glycoprotein B - sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Postfusion conformation structure of the Herpes Simplex Virus...

Fileemd_52863_half_map_1.map
AnnotationPostfusion conformation structure of the Herpes Simplex Virus 2 glycoprotein B - Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Postfusion conformation structure of the Herpes Simplex Virus...

Fileemd_52863_half_map_2.map
AnnotationPostfusion conformation structure of the Herpes Simplex Virus 2 glycoprotein B - Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human herpesvirus 2 strain 333

EntireName: Human herpesvirus 2 strain 333
Components
  • Virus: Human herpesvirus 2 strain 333
    • Protein or peptide: Envelope glycoprotein B

-
Supramolecule #1: Human herpesvirus 2 strain 333

SupramoleculeName: Human herpesvirus 2 strain 333 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10313 / Sci species name: Human herpesvirus 2 strain 333 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1
Details: Full-length protein + 3C protease cleavage site + Strep-Tag II
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2 strain 333 / Strain: 333
Molecular weightTheoretical: 104.648422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGGGLICAL VVGALVAAVA SAAPAAPAAP RASGGVAATV AANGGPASRP PPVPSPATTK ARKRKTKKPP KRPEATPPPD ANATVAAGH ATLRAHLREI KVENADAQFY VCPPPTGATV VQFEQPRRCP TRPEGQNYTE GIAVVFKENI APYKFKATMY Y KDVTVSQV ...String:
MRGGGLICAL VVGALVAAVA SAAPAAPAAP RASGGVAATV AANGGPASRP PPVPSPATTK ARKRKTKKPP KRPEATPPPD ANATVAAGH ATLRAHLREI KVENADAQFY VCPPPTGATV VQFEQPRRCP TRPEGQNYTE GIAVVFKENI APYKFKATMY Y KDVTVSQV WFGHRYSQFM GIFEDRAPVP FEEVIDKINA KGVCRSTAKY VRNNMETTAF HRDDHETDME LKPAKVATRT SR GWHTTDL KYNPSRVEAF HRYGTTVNCI VEEVDARSVY PYDEFVLATG DFVYMSPFYG YREGSHTEHT SYAADRFKQV DGF YARDLT TKARATSPTT RNLLTTPKFT VAWDWVPKRP AVCTMTKWQE VDEMLRAEYG GSFRFSSDAI STTFTTNLTQ YSLS RVDLG DCIGRDAREA IDRMFARKYN ATHIKVGQPQ YYLATGGFLI AYQPLLSNTL AELYVREYMR EQDRKPRNAT PAPLR EAPS ANASVERIKT TSSIEFARLQ FTYNHIQRHV NDMLGRIAVA WCELQNHELT LWNEARKLNP NAIASATVGR RVSARM LGD VMAVSTCVPV APDNVIVQNS MRVSSRPGTC YSRPLVSFRY EDQGPLIEGQ LGENNELRLT RDALEPCTVG HRRYFIF GG GYVYFEEYAY SHQLSRADVT TVSTFIDLNI TMLEDHEFVP LEVYTRHEIK DSGLLDYTEV QRRNQLHDLR FADIDTVI R ADANAAMFAG LCAFFEGMGD LGRAVGKVVM GVVGGVVSAV SGVSSFMSNP FGALAVGLLV LAGLVAAFFA FRYVLQLQR NPMKALYPLT TKELKTSDPG GVGGEGEEGA EGGGFDEAKL AEAREMIRYM ALVSAMERTE HKARKKGTSA LLSSKVTNMV LRKRNKARY SPLHNEDEAG DEDELGTLEV LFQGPGGSGS AWSHPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: Envelope glycoprotein B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
300.0 mMNaClSodium Chloride
5.0 mMH2NCOCH2CH2CH(NH2)CO2HL-Glutamin
5.0 mMC6H14N4O2HClL-Arginine, hydrochloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was coated with carbon prior to use
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14886 / Average exposure time: 2.197 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3833942
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0) / Number images used: 323536
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 38.46
Output model

PDB-9ih8:
HSV-2 postfusion glycoprotein B

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more