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- EMDB-70692: C Capsid C1 Portal Vertex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70692
TitleC Capsid C1 Portal Vertex
Map data
Sample
  • Complex: C1 Capsid Portal Vertex
KeywordsComplex / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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 18, 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_70692.png

Downloads & links

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Map

FileDownload / File: emd_70692.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: 0.1
Minimum - Maximum-0.2078868 - 0.3773764
Average (Standard dev.)0.0036011057 (±0.035159145)
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_70692_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70692_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_70692_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 : C1 Capsid Portal Vertex

EntireName: C1 Capsid Portal Vertex
Components
  • Complex: C1 Capsid Portal Vertex

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Supramolecule #1: C1 Capsid Portal Vertex

SupramoleculeName: C1 Capsid Portal Vertex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 19345
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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