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- EMDB-70678: Herpes simplex virus type 1 (HSV-1) A-capsid pUL6 portal protein,... -

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Basic information

Entry
Database: EMDB / ID: EMD-70678
TitleHerpes simplex virus type 1 (HSV-1) A-capsid pUL6 portal protein, dodecameric complex
Map data
Sample
  • Complex: Dodecameric complex of pUL6 with bound loops from scaffolding protein
    • Protein or peptide: Capsid scaffolding protein
    • Protein or peptide: Capsid portal protein
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / chromosome organization / virion component / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Herpesvirus portal protein / Herpesvirus UL6 like / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21)
Similarity search - Domain/homology
Capsid portal protein / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsCrofut EH / Kashyap S / Stevens A / Jih J / Liu Y-T / Zhou ZH
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151055 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5T32AR071307 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM145388 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
CitationJournal: J Virol / Year: 2025
Title: Structure of a new capsid form and comparison with A-, B-, and C-capsids clarify herpesvirus assembly.
Authors: Alexander Stevens / Saarang Kashyap / Ethan Crofut / Ana Lucia Alvarez-Cabrera / Jonathan Jih / Yun-Tao Liu / Z Hong Zhou /
Abstract: Three capsid types have been recognized from the nuclei of herpesvirus-infected cells: empty A-capsids, scaffolding-containing B-capsids, and DNA-filled C-capsids. Despite progress in determining ...Three capsid types have been recognized from the nuclei of herpesvirus-infected cells: empty A-capsids, scaffolding-containing B-capsids, and DNA-filled C-capsids. Despite progress in determining atomic structures of these capsids and extracellular virions in recent years, debate persists concerning the origins and temporal relationships among these capsids during capsid assembly and genome packaging. Here, we have imaged over 300,000 capsids of herpes simplex virus type 1 by cryogenic electron microscopy (cryoEM) and exhaustively classified them to characterize the structural heterogeneity of the DNA-translocating portal complex and their functional states. The resultant atomic structures reveal not only the expected A-, B-, and C-capsids but also capsids with portal vertices similar to C-capsids but no resolvable genome in the capsid lumen, which we named D-capsids. The dodecameric dsDNA-translocating portal complex varies across these capsid types in their radial positions in icosahedral capsids and exhibits structural dynamics within each capsid type. In D-capsids, terminal DNA density exists in multiple conformations including one reminiscent of that in C-capsids, suggesting D-capsids are products of failed DNA retention. This interpretation is supported by varying amounts of DNA outside individual D-capsids and by the correlation of capsid counts observed of infected cell nuclei and those after purification. Additionally, an "anchoring" segment of the scaffold protein is resolved interacting with the portal baskets of A- and B-capsids but not D- and C-capsids. Taken together, our data indicate that A-capsids arise from failed DNA packaging and D-capsids from failed genome retention, clarifying the origins of empty capsids in herpesvirus assembly.IMPORTANCEAs the prototypical herpesvirus, herpes simplex virus 1 (HSV-1) exhibits a global seroprevalence of 67% and approaching 90% in some localities. Herpesvirus infections can cause devastating cancers and birth defects, with HSV-1 infections leading to cold sores among the general population worldwide and blindness in developing nations. Here, we present atomic structures of the capsids sorted out from the nuclear isolates of HSV-1 infected cells, including the previously recognized A-, B-, and C-capsids, as well as the newly identified D-capsid. The structures show the details of protein-protein and protein-DNA interactions within each capsid type and the positional and interactional variability of the viral DNA-translocating portal vertex among these capsids. Importantly, our findings suggest that A-capsids are products of failed dsDNA packaging and D-capsids of failed genome retention. Together, the high-resolution 3D structures clarify the processes of genome packaging, maintenance, and ejection during capsid assembly, which are conserved across all herpesviruses.
History
DepositionMay 16, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70678.png

Downloads & links

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Map

FileDownload / File: emd_70678.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.228
Minimum - Maximum-1.5983729 - 2.326426
Average (Standard dev.)0.0041399496 (±0.057024702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70678_msk_1.map
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Half map: #2

Fileemd_70678_half_map_1.map
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Half map: #1

Fileemd_70678_half_map_2.map
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Sample components

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Entire : Dodecameric complex of pUL6 with bound loops from scaffolding protein

EntireName: Dodecameric complex of pUL6 with bound loops from scaffolding protein
Components
  • Complex: Dodecameric complex of pUL6 with bound loops from scaffolding protein
    • Protein or peptide: Capsid scaffolding protein
    • Protein or peptide: Capsid portal protein

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Supramolecule #1: Dodecameric complex of pUL6 with bound loops from scaffolding protein

SupramoleculeName: Dodecameric complex of pUL6 with bound loops from scaffolding protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS

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Macromolecule #1: Capsid scaffolding protein

MacromoleculeName: Capsid scaffolding protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS
Molecular weightTheoretical: 66.501609 KDa
SequenceString: MAADAPGDRM EEPLPDRAVP IYVAGFLALY DSGDSGELAL DPDTVRAALP PDNPLPINVD HRAGCEVGRV LAVVDDPRGP FFVGLIACV QLERVLETAA SAAIFERRGP PLSREERLLY LITNYLPSVS LATKRLGGEA HPDRTLFAHV ALCAIGRRLG T IVTYDTGL ...String:
MAADAPGDRM EEPLPDRAVP IYVAGFLALY DSGDSGELAL DPDTVRAALP PDNPLPINVD HRAGCEVGRV LAVVDDPRGP FFVGLIACV QLERVLETAA SAAIFERRGP PLSREERLLY LITNYLPSVS LATKRLGGEA HPDRTLFAHV ALCAIGRRLG T IVTYDTGL DAAIAPFRHL SPASREGARR LAAEAEIALS GRTWAPGVEA LTHTLLSTAV NNMMLRDRWS LVAERRRQAG IA GHTYLQA SEKFKMWGAE PVSAPARGYK NGAPESTDIP PGSIAAAPQG DRCPIVRQRG VALSPVLPPM NPVPTSGTPA PAP PGDGSY LWIPASHYNQ LVAGHAAPQP QPHSAFGFPA AAGAVAYGPH GAGLSQHYPP HVAHQYPGVL FSGPSPLEAQ IAAL VGAIA ADRQAGGQPA AGDPGVRGSG KRRRYEAGPS ESYCDQDEPD ADYPYYPGEA RGGPRGVDSR RAARQSPGTN ETITA LMGA VTSLQQELAH MRARTSAPYG MYTPVAHYRP QVGEPEPTTT HPALCPPEAV YRPPPHSAPY GPPQGPASHA PTPPYA PAA CPPGPPPPPC PSTQTRAPLP TEPAFPPAAT GSQPEASNAE AGALVNASSA AHVDVDTARA ADLFVSQMMG AR

UniProtKB: Capsid scaffolding protein

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Macromolecule #2: Capsid portal protein

MacromoleculeName: Capsid portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS
Molecular weightTheoretical: 74.178523 KDa
SequenceString: MTAPRSWAPT TRARGDTEAL CSPEDGWVKV HPTPGTMLFR EILHGQLGYT EGQGVYNVVR SSEATTRQLQ AAIFHALLNA TTYRDLEAD WLGHVAARGL QPQRLVRRYR NAREADIAGV AERVFDTWRN TLRTTLLDFA HGLVACFAPG GPSGPSSFPK Y IDWLTCLG ...String:
MTAPRSWAPT TRARGDTEAL CSPEDGWVKV HPTPGTMLFR EILHGQLGYT EGQGVYNVVR SSEATTRQLQ AAIFHALLNA TTYRDLEAD WLGHVAARGL QPQRLVRRYR NAREADIAGV AERVFDTWRN TLRTTLLDFA HGLVACFAPG GPSGPSSFPK Y IDWLTCLG LVPILRKRQE GGVTQGLRAF LKQHPLTRQL ATVAEAAERA GPGFFELALA FDSTRVADYD RVYIYYNHRR GD WLVRDPI SGQRGECLVL WPPLWTGDRL VFDSPVQRLF PEIVACHSLR EHAHVCRLRN TASVKVLLGR KSDSERGVAG AAR VVNKVL GEDDETKAGS AASRLVRLII NMKGMRHVGD INDTVRSYLD EAGGHLIDAP AVDGTLPGFG KGGNSRGSAG QDQG GRAPQ LRQAFRTAVV NNINGVLEGY INNLFGTIER LRETNAGLAT QLQERDRELR RATAGALERQ QRAADLAAES VTGGC GSRP AGADLLRADY DIIDVSKSMD DDTYVANSFQ HPYIPSYAQD LERLSRLWEH ELVRCFKILC HRNNQGQETS ISYSSG AIA AFVAPYFESV LRAPRVGAPI TGSDVILGEE ELWDAVFKKT RLQTYLTDIA ALFVADVQHA ALPPPPSPVG ADFRPGA SP RGRSRSRSPG RTAPGAPDQG GGIGHRDGRR DGRR

UniProtKB: Capsid portal protein

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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
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 363576
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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