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- PDB-9sv8: Herpes simplex virus 2 delta28-73 glycoprotein C ectodomain in co... -

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Basic information

Entry
Database: PDB / ID: 9sv8
TitleHerpes simplex virus 2 delta28-73 glycoprotein C ectodomain in complex with C3b
Components
  • Complement C3 beta chain
  • Complement C3b alpha' chain
  • Envelope glycoprotein C
KeywordsVIRAL PROTEIN / Protein complex / domains 1 and 2 of gC2 with C3b.
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsRojas Rechy, M.H. / Atanasiu, D. / Hook, L.M. / Cairns, M.T. / Saw, W.T. / Cahill, A. / Guo, Z. / Calabrese, A.N. / Ranson, N.A. / Friedman, H.M. ...Rojas Rechy, M.H. / Atanasiu, D. / Hook, L.M. / Cairns, M.T. / Saw, W.T. / Cahill, A. / Guo, Z. / Calabrese, A.N. / Ranson, N.A. / Friedman, H.M. / Cohen, G.H. / Fontana, J.
Funding support Spain, European Union, Mexico, United Kingdom, 9items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein C
B: Complement C3 beta chain
C: Complement C3b alpha' chain


Theoretical massNumber of molelcules
Total (without water)227,2133
Polymers227,2133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Envelope glycoprotein C / Glycoprotein F


Mass: 51729.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The gC2 ectodomain used contains a deletion from the amino-acids 28-73
Source: (gene. exp.) Human alphaherpesvirus 2 / Gene: gC, UL44 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03173
#2: Protein Complement C3 beta chain


Mass: 71409.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Homo sapiens (human) / References: UniProt: P01024
#3: Protein Complement C3b alpha' chain


Mass: 104074.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Homo sapiens (human) / References: UniProt: P01024
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Glycoprotein C of Herpes Simplex Virus, domains 1 and 2 with human complement protein C3b.COMPLEXGlycoprotein C has a deletion in the amino-acids 28-73all0MULTIPLE SOURCES
2Herpes simplex virus 2, delta28-73 glycoprotein C ectodomainCOMPLEXgC2 has a deletion in the amino-acids 28-73#11RECOMBINANT
3Complement human protein C3bCOMPLEXChains A and B from complement protein C3b.#2-#31NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.239 MDaYES
210.059 MDaYES
310.180 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Human alphaherpesvirus 210310
32Human alphaherpesvirus 210310
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Cricetulus griseus (Chinese hamster)10029
32Cricetulus griseus (Chinese hamster)10029
43Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8.0particle selection
2PHENIX1.20.1_4487model refinement
5CTFFIND4.1CTF correction
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 466599 / Symmetry type: POINT
RefinementHighest resolution: 3.56 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049326
ELECTRON MICROSCOPYf_angle_d0.65812655
ELECTRON MICROSCOPYf_dihedral_angle_d4.1971259
ELECTRON MICROSCOPYf_chiral_restr0.0451446
ELECTRON MICROSCOPYf_plane_restr0.0061636

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