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- PDB-30je: Herpes simplex virus 2 delta28-73 glycoprotein C ectodomain in co... -

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Basic information

Entry
Database: PDB / ID: 30je
TitleHerpes simplex virus 2 delta28-73 glycoprotein C ectodomain in complex with C3b
Components
  • Complement C3
  • Complement C3 beta chain
  • Envelope glycoprotein C
KeywordsVIRAL PROTEIN / Protein complex / complement 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 / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity ...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 / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 / positive regulation of lipid storage / complement activation, GZMK pathway / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement receptor mediated signaling pathway / adhesion receptor-mediated virion attachment to host cell / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / B cell activation / amyloid-beta clearance / complement activation, classical pathway / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of protein phosphorylation / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / receptor ligand activity / signaling receptor binding / Neutrophil degranulation / symbiont entry into host cell / virion membrane / cell surface / signal transduction / protein-containing complex / : / extracellular exosome / extracellular region / 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 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site ...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 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / 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: 3.5 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, Mexico, United Kingdom, 8items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2023-149259NB-I00 Spain
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: To Be Published
Title: Herpes simplex virus 2 delta28-73 glycoprotein C ectodomain in complex with C3b
Authors: 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.
History
DepositionApr 29, 2026Deposition site: PDBE / Processing site: PDBE
SupersessionMay 6, 2026ID: 9SV8
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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 C3


Theoretical massNumber of molelcules
Total (without water)228,0413
Polymers228,0413
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: 52558.168 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 C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 104073.164 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
IDNameTypeDetails (eV)Entity 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-#32RECOMBINANT
Molecular weightValue: 0.239 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Human alphaherpesvirus 210310
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Cricetulus griseus (Chinese hamster)10029
33Homo sapiens (human)9606
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
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 466599 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048092
ELECTRON MICROSCOPYf_angle_d0.56110952
ELECTRON MICROSCOPYf_dihedral_angle_d4.261066
ELECTRON MICROSCOPYf_chiral_restr0.0471274
ELECTRON MICROSCOPYf_plane_restr0.0041379

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