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- EMDB-59277: Cryo-ET STA of mature HERV-K hexameric capsomer -

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Basic information

Entry
Database: EMDB / ID: EMD-59277
TitleCryo-ET STA of mature HERV-K hexameric capsomer
Map data
Sample
  • Virus: Human endogenous retrovirus K
KeywordsViral Capsid / Human Endogenous Retrovirus / VIRAL PROTEIN
Biological speciesHuman endogenous retrovirus K
Methodsubtomogram averaging / cryo EM / Resolution: 6.2 Å
AuthorsLyu C / Shen Y / Hou Z / Zhang P
Funding support United Kingdom, China, 2 items
OrganizationGrant numberCountry
Wellcome Trust311427/Z/24/Z United Kingdom
Chinese Scholarship CouncilCNR00051 China
CitationJournal: To Be Published
Title: Structural Insights into Native, Mature Human Endogenous Retrovirus K (HERV-K) Capsids
Authors: Lyu C / Peeples CA / Zhang Z / Shen Y / Hou Z / Harding EF / Hope J / Perilla JR / Katzourakis A / Zhang P
History
DepositionAug 1, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59277.png

Downloads & links

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Map

FileDownload / File: emd_59277.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.55 Å/pix.
x 216 pix.
= 335.664 Å		1.55 Å/pix.
x 216 pix.
= 335.664 Å		1.55 Å/pix.
x 216 pix.
= 335.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.554 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 33.0
Minimum - Maximum-89.953109999999995 - 106.952250000000006
Average (Standard dev.)0.10660299 (±2.4449768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 335.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_59277_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_59277_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_59277_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 : Human endogenous retrovirus K

EntireName: Human endogenous retrovirus K
Components
  • Virus: Human endogenous retrovirus K

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Supramolecule #1: Human endogenous retrovirus K

SupramoleculeName: Human endogenous retrovirus K / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 45617 / Sci species name: Human endogenous retrovirus K / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.2) / Number subtomograms used: 31450
ExtractionNumber tomograms: 138 / Number images used: 37724 / Software: (Name: emClarity, RELION (ver. 4.0.2))
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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