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- EMDB-59279: Cryo-EM structure of native, mature HERV-K pentameric capsomer -

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Basic information

Entry
Database: EMDB / ID: EMD-59279
TitleCryo-EM structure of native, mature HERV-K pentameric capsomer
Map data
Sample
  • Virus: Human endogenous retrovirus K
    • Protein or peptide: Endogenous retrovirus group K member 8 Gag polyprotein
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsViral Capsid / Human Endogenous Retrovirus / VIRAL PROTEIN
Function / homology
Function and homology information


viral process / nucleic acid binding / structural molecule activity / zinc ion binding / plasma membrane
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Endogenous retrovirus group K member 8 Gag polyprotein
Similarity search - Component
Biological speciesHuman endogenous retrovirus K
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsLyu C / Shen Y / 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 2, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59279.png

Downloads & links

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Map

FileDownload / File: emd_59279.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 336 pix.
= 278.544 Å		0.83 Å/pix.
x 336 pix.
= 278.544 Å		0.83 Å/pix.
x 336 pix.
= 278.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.127
Minimum - Maximum-0.43899843 - 0.7022918
Average (Standard dev.)0.0006736886 (±0.019583872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 278.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_59279_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_59279_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_59279_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
    • Protein or peptide: Endogenous retrovirus group K member 8 Gag polyprotein
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: Human endogenous retrovirus K

SupramoleculeName: Human endogenous retrovirus K / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / 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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Macromolecule #1: Endogenous retrovirus group K member 8 Gag polyprotein

MacromoleculeName: Endogenous retrovirus group K member 8 Gag polyprotein
type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human endogenous retrovirus K
Molecular weightTheoretical: 26.185752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PVTLEPMPPG EGAQEGEPPT VEARYKSFSI KMLKDMKEGV KQYGPNSPYM RTLLDSIAHG HRLIPYDWEI LAKSSLSPSQ FLQFKTWWI DGVQEQVRRN RAANPPVNID ADQLLGIGQN WSTISQQALM QNEAIEQVRA ICLRAWEKIQ DPGSTCPSFN T VRQGSKEP ...String:
PVTLEPMPPG EGAQEGEPPT VEARYKSFSI KMLKDMKEGV KQYGPNSPYM RTLLDSIAHG HRLIPYDWEI LAKSSLSPSQ FLQFKTWWI DGVQEQVRRN RAANPPVNID ADQLLGIGQN WSTISQQALM QNEAIEQVRA ICLRAWEKIQ DPGSTCPSFN T VRQGSKEP YPDFVARLQD VAQKSIADEK ARKVIVELMA YENANPECQS AIKPLKGKVP AGSDVISEYV KACDGIG

UniProtKB: Endogenous retrovirus group K member 8 Gag polyprotein

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Macromolecule #2: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1827160
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60840
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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