[English] 日本語
Yorodumi
- EMDB-55293: Herpes simplex virus 2 delta28-73 glycoprotein C (focus classific... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55293
TitleHerpes simplex virus 2 delta28-73 glycoprotein C (focus classification) ectodomain in complex with C3b
Map data
Sample
  • Complex: Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with human complement protein C3b.
    • Complex: Herpes simplex virus 2, delta28-73 glycoprotein C ectodomain
    • Complex: Complement human protein C3b
KeywordsProtein complex / domains 1 and 2 of gC2 with C3b. / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsRojas Rechy MH / Atanasiu D / Hook LM / Cairns MT / Saw WT / Cahill A / Guo Z / Calabrese AN / Ranson NA / Friedman HM ...Rojas Rechy MH / Atanasiu D / Hook LM / Cairns MT / Saw WT / Cahill A / Guo Z / Calabrese AN / Ranson NA / Friedman HM / Cohen GH / Fontana J
Funding support Spain, European Union, Mexico, United Kingdom, 9 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2023-149259NB-I00, Spain
European Regional Development FundPID2023-149259NB-I00European Union
Agencia Estatal de Investigacion (AEI)PID2023-149259NB-I00 Spain
Consejo Nacional de Ciencia y Tecnologia (CONACYT)773992 Mexico
Engineering and Physical Sciences Research CouncilEP/W524372/1 United Kingdom
Wellcome Trust220628/Z/20/Z United Kingdom
Wellcome Trust221524/Z/20/Z United Kingdom
Wellcome Trust223810/Z/21/Z United Kingdom
Wolfson FoundationPR/jw/md/22597 United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Unveiling the unique interaction mechanism of herpes simplex virus 2 glycoprotein C with C3b.
Authors: Moisés Hasim Rojas Rechy / Doina Atanasiu / Lauren M Hook / Tina M Cairns / Wan Ting Saw / Adam Cahill / Zilin Guo / Antonio N Calabrese / Neil A Ranson / Harvey M Friedman / Gary H Cohen / Juan Fontana /
Abstract: The complement cascade is part of the first line of defence against viral infections, and many viruses have evolved to block it. For example, glycoprotein C (gC) from Herpes Simplex Virus 1 and 2 ...The complement cascade is part of the first line of defence against viral infections, and many viruses have evolved to block it. For example, glycoprotein C (gC) from Herpes Simplex Virus 1 and 2 (gC1 and gC2) facilitates infection by modulating the complement cascade through an interaction with C3b. gC is also involved in attachment and other viral processes. However, our understanding of the molecular mechanisms of gC have been limited due to the absence of a structure. AlphaFold predicts that gC contains a disordered N-terminus and three immunoglobulin-like domains. Here, we generated various gC2 constructs and demonstrated that gC2 domains 1 and 2 are necessary and sufficient to interact with C3b and block the alternative pathway. A gC2 construct lacking the N-terminus in complex with C3b was characterised by cryo-EM at 3.6 Å, providing the first structure for gC2, and revealing that the interaction is predominantly driven by gC2 domain 2 and the MG8 domain of C3b. This structure was confirmed by cross-linking mass spectrometry and by using C3b-blocking antibodies that recognised gC2 linear epitopes at the interface with C3b. Overall, the gC-C3b interaction is different from other C3b-interacting partners, providing a novel mechanism to regulate the complement cascade.
History
DepositionOct 3, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55293.png

Downloads & links

-
Map

FileDownload / File: emd_55293.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.216
Minimum - Maximum-1.1240315 - 1.9417675
Average (Standard dev.)0.009311961 (±0.042969156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 222.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55293_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_55293_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55293_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with huma...

EntireName: Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with human complement protein C3b.
Components
  • Complex: Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with human complement protein C3b.
    • Complex: Herpes simplex virus 2, delta28-73 glycoprotein C ectodomain
    • Complex: Complement human protein C3b

-
Supramolecule #1: Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with huma...

SupramoleculeName: Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with human complement protein C3b.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Glycoprotein C has a deletion in the amino-acids 28-73
Source (natural)Organism: Human alphaherpesvirus 2
Molecular weightTheoretical: 180 KDa

-
Supramolecule #2: Herpes simplex virus 2, delta28-73 glycoprotein C ectodomain

SupramoleculeName: Herpes simplex virus 2, delta28-73 glycoprotein C ectodomain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: gC2 has a deletion in the amino-acids 28-73
Source (natural)Organism: Human alphaherpesvirus 2

-
Supramolecule #3: Complement human protein C3b

SupramoleculeName: Complement human protein C3b / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Chains A and B from complement protein C3b.
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 466599
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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