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- EMDB-57830: Herpes simplex virus 2 delta28-73 glycoprotein C ectodomain in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-57830
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
      • Complex: Complement human protein C3b
        • Protein or peptide: Complement C3 beta chain
        • Protein or peptide: Complement C3
      • Protein or peptide: Envelope glycoprotein C
KeywordsProtein complex / complement protein / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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, Mexico, United Kingdom, 8 items
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 MH / Atanasiu D / Hook LM / Cairns MT / Saw WT / Cahill A / Guo Z / Calabrese AN / Ranson NA / Friedman HM / Cohen GH / Fontana J
History
DepositionApr 29, 2026-
SupersessionMay 6, 2026ID: EMD-55245
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57830.png

Downloads & links

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Map

FileDownload / File: emd_57830.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: 0.212
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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Half map: #2

Fileemd_57830_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57830_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

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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
Molecular weightTheoretical: 239 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: 2 / 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: 52.558168 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 RRLRH HHHH H

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 C3

MacromoleculeName: Complement C3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.073164 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 TPSGCGEQNM 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 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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