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- EMDB-70679: Herpes simplex virus type 1 (HSV-1) B-capsid pUL6 portal protein,... -

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Basic information

Entry
Database: EMDB / ID: EMD-70679
TitleHerpes simplex virus type 1 (HSV-1) B-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: 3.5 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: To Be Published
Title: Structure of a new capsid form and comparison with A-, B- and C-capsids clarify herpesvirus assembly
Authors: Stevens A / Kashyap S / Crofut EH / Alvarez-Cabrera AL / Jih J / Liu Y-T / Zhou ZH
History
DepositionMay 16, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70679.png

Downloads & links

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Map

FileDownload / File: emd_70679.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.187
Minimum - Maximum-1.4015248 - 2.0118942
Average (Standard dev.)0.003188696 (±0.044484727)
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_70679_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70679_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70679_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 : 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: 74.162523 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 INDTVRAYLD 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 799092
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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