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- EMDB-55245: Herpes simplex virus 2 delta28-73 glycoprotein C ectodomain in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-55245
TitleHerpes simplex virus 2 delta28-73 glycoprotein C 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
      • Protein or peptide: Envelope glycoprotein C
    • Complex: Complement human protein C3b
      • Protein or peptide: Complement C3 beta chain
      • Protein or peptide: Complement C3b alpha' chain
KeywordsProtein complex / domains 1 and 2 of gC2 with C3b. / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host complement activation / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment ...symbiont-mediated suppression of host complement activation / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / adhesion receptor-mediated virion attachment to host cell / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of protein phosphorylation / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / Neutrophil degranulation / symbiont entry into host cell / virion membrane / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Glycoprotein C/ glycoprotein A / Marek's disease glycoprotein A / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 ...Glycoprotein C/ glycoprotein A / Marek's disease glycoprotein A / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C3 / Envelope glycoprotein C
Similarity search - Component
Biological speciesHuman alphaherpesvirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 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 2, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55245.png

Downloads & links

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Map

FileDownload / File: emd_55245.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

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.249
Minimum - Maximum-1.4427714 - 2.3471453
Average (Standard dev.)0.0044899704 (±0.05067087)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_55245_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_55245_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_55245_half_map_2.map
Projections & Slices
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Sample components

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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
      • Protein or peptide: Envelope glycoprotein C
    • Complex: Complement human protein C3b
      • Protein or peptide: Complement C3 beta chain
      • Protein or peptide: Complement C3b alpha' chain

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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: all
Details: Glycoprotein C has a deletion in the amino-acids 28-73
Source (natural)Organism: Human alphaherpesvirus 2
Molecular weightTheoretical: 180 KDa

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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

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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)

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Macromolecule #1: Envelope glycoprotein C

MacromoleculeName: Envelope glycoprotein C / type: protein_or_peptide / ID: 1
Details: The gC2 ectodomain used contains a deletion from the amino-acids 28-73
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 2
Molecular weightTheoretical: 51.729297 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MALGRVGLTV GLWGLLWVGV VVVLANASPG RTITVGPRGN ASNAAPSVPR NRSAPRTTPT PPQPRKATKS KASTAKPAPP PKTGPPKTS SEPVRCNRHD PLARYGSRVQ IRCRFPNSTR TESRLQIWRY ATATDAEIGT APSLEEVMVN VSAPPGGQLV Y DSAPNRTD ...String:
MALGRVGLTV GLWGLLWVGV VVVLANASPG RTITVGPRGN ASNAAPSVPR NRSAPRTTPT PPQPRKATKS KASTAKPAPP PKTGPPKTS SEPVRCNRHD PLARYGSRVQ IRCRFPNSTR TESRLQIWRY ATATDAEIGT APSLEEVMVN VSAPPGGQLV Y DSAPNRTD PHVIWAEGAG PGASPRLYSV VGPLGRQRLI IEELTLETQG MYYWVWGRTD RPSAYGTWVR VRVFRPPSLT IH PHAVLEG QPFKATCTAA TYYPGNRAEF VWFEDGRRVF DPAQIHTQTQ ENPDGFSTVS TVTSAAVGGQ GPPRTFTCQL TWH RDSVSF SRRNASGTAS VLPRPTITME FTGDHAVCTA GCVPEGVTFA WFLGDDSSPA EKVAVASQTS CGRPGTATIR STLP VSYEQ TEYICRLAGY PDGIPVLEHH GSHQPPPRDP TERQVIRAVE GAGIGVAVLV AVVLAGTAVV YLTHASSVRY RRLR

UniProtKB: Envelope glycoprotein C

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Macromolecule #2: Complement C3 beta chain

MacromoleculeName: Complement C3 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.409359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQAT FGTQVVEKVV LVSLQSGYLF IQTDKTIYTP GSTVLYRIFT VNHKLLPVGR TVMVNIENPE GIPVKQDSLS S QNQLGVLP ...String:
SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQAT FGTQVVEKVV LVSLQSGYLF IQTDKTIYTP GSTVLYRIFT VNHKLLPVGR TVMVNIENPE GIPVKQDSLS S QNQLGVLP LSWDIPELVN MGQWKIRAYY ENSPQQVFST EFEVKEYVLP SFEVIVEPTE KFYYIYNEKG LEVTITARFL YG KKVEGTA FVIFGIQDGE QRISLPESLK RIPIEDGSGE VVLSRKVLLD GVQNLRAEDL VGKSLYVSAT VILHSGSDMV QAE RSGIPI VTSPYQIHFT KTPKYFKPGM PFDLMVFVTN PDGSPAYRVP VAVQGEDTVQ SLTQGDGVAK LSINTHPSQK PLSI TVRTK KQELSEAEQA TRTMQALPYS TVGNSNNYLH LSVLRTELRP GETLNVNFLL RMDRAHEAKI RYYTYLIMNK GRLLK AGRQ VREPGQDLVV LPLSITTDFI PSFRLVAYYT LIGASGQREV VADSVWVDVK DSCVGSLVVK SGQSEDRQPV PGQQMT LKI EGDHGARVVL VAVDKGVFVL NKKNKLTQSK IWDVVEKADI GCTPGSGKDY AGVFSDAGLT FTSSSGQQTA QRAELQC PQ PAA

UniProtKB: Complement C3

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Macromolecule #3: Complement C3b alpha' chain

MacromoleculeName: Complement C3b alpha' chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.074148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SNLDEDIIAE ENIVSRSEFP ESWLWNVEDL KEPPKNGIST KLMNIFLKDS ITTWEILAVS MSDKKGICVA DPFEVTVMQD FFIDLRLPY SVVRNEQVEI RAVLYNYRQN QELKVRVELL HNPAFCSLAT TKRRHQQTVT IPPKSSLSVP YVIVPLKTGL Q EVEVKAAV ...String:
SNLDEDIIAE ENIVSRSEFP ESWLWNVEDL KEPPKNGIST KLMNIFLKDS ITTWEILAVS MSDKKGICVA DPFEVTVMQD FFIDLRLPY SVVRNEQVEI RAVLYNYRQN QELKVRVELL HNPAFCSLAT TKRRHQQTVT IPPKSSLSVP YVIVPLKTGL Q EVEVKAAV YHHFISDGVR KSLKVVPEGI RMNKTVAVRT LDPERLGREG VQKEDIPPAD LSDQVPDTES ETRILLQGTP VA QMTEDAV DAERLKHLIV TPSGCGEENM IGMTPTVIAV HYLDETEQWE KFGLEKRQGA LELIKKGYTQ QLAFRQPSSA FAA FVKRAP STWLTAYVVK VFSLAVNLIA IDSQVLCGAV KWLILEKQKP DGVFQEDAPV IHQEMIGGLR NNNEKDMALT AFVL ISLQE AKDICEEQVN SLPGSITKAG DFLEANYMNL QRSYTVAIAG YALAQMGRLK GPLLNKFLTT AKDKNRWEDP GKQLY NVEA TSYALLALLQ LKDFDFVPPV VRWLNEQRYY GGGYGSTQAT FMVFQALAQY QKDAPDHQEL NLDVSLQLPS RSSKIT HRI HWESASLLRS EETKENEGFT VTAEGKGQGT LSVVTMYHAK AKDQLTCNKF DLKVTIKPAP ETEKRPQDAK NTMILEI CT RYRGDQDATM SILDISMMTG FAPDTDDLKQ LANGVDRYIS KYELDKAFSD RNTLIIYLDK VSHSEDDCLA FKVHQYFN V ELIQPGAVKV YAYYNLEESC TRFYHPEKED GKLNKLCRDE LCRCAEENCF IQKSDDKVTL EERLDKACEP GVDYVYKTR LVKVQLSNDF DEYIMAIEQT IKSGSDEVQV GQQRTFISPI KCREALKLEE KKHYLMWGLS SDFWGEKPNL SYIIGKDTWV EHWPEEDEC QDEENQKQCQ DLGAFTESMV VFGCPN

UniProtKB: Complement C3

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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

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

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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: 3.56 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)

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