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- EMDB-73989: The cryo-EM structure of Pakpunavirus P7-1 head(capsid:decoration... -

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Basic information

Entry
Database: EMDB / ID: EMD-73989
TitleThe cryo-EM structure of Pakpunavirus P7-1 head(capsid:decoration protein)
Map data
Sample
  • Virus: Pakpunavirus
    • Protein or peptide: Capsid protein
    • Protein or peptide: Decorating protein
KeywordsPakpunavirus P7-1 / Cryo-EM / in situ / structure / head / viral protein
Biological speciesPakpunavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLi F / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: To be published
Title: The cryo-EM structure of Pakpunavirus P7-1 head(capsid:decoration protein)
Authors: Li F / Cingolani G
History
DepositionNov 20, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73989.png

Downloads & links

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Map

FileDownload / File: emd_73989.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.84 Å		1.36 Å/pix.
x 320 pix.
= 435.84 Å		1.36 Å/pix.
x 320 pix.
= 435.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.362 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.07013275 - 0.11797494
Average (Standard dev.)0.00028948422 (±0.008956377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73989_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_73989_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 : Pakpunavirus

EntireName: Pakpunavirus
Components
  • Virus: Pakpunavirus
    • Protein or peptide: Capsid protein
    • Protein or peptide: Decorating protein

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Supramolecule #1: Pakpunavirus

SupramoleculeName: Pakpunavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1921407 / Sci species name: Pakpunavirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 39.419012 KDa
SequenceString: MANTRSYLND GQFYIADQTE NLLIIPNTWT LVENMGVFTS EGVTQNTVQF EEIETRYGLV KDAIRGTRHQ VASDQRRQLR AFAIPHFNQ DDYITPEDIQ GKRAFGADRE ETLNEVRARK LETIRRNWAN TAEVASVSAI VTGKSYAPAG TIEYDWYDLM G KTRKVVGF ...String:
MANTRSYLND GQFYIADQTE NLLIIPNTWT LVENMGVFTS EGVTQNTVQF EEIETRYGLV KDAIRGTRHQ VASDQRRQLR AFAIPHFNQ DDYITPEDIQ GKRAFGADRE ETLNEVRARK LETIRRNWAN TAEVASVSAI VTGKSYAPAG TIEYDWYDLM G KTRKVVGF DLTNPTADVM GKTEEIFVHM QDNSQDGLIR GDFVALCSPE FFTALINHPS IKEFYKAYQA SPQYWRERLT AR GLDLRFR EFYFGNIHFI EYRGVDPYGN RLIPAGDAYF IPTDSGDLFA RYFGPGSTFD DLGTLGKELY ATERMAEDRR SIL IETESN FIHVLRRPQM IVRGTVNA

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Macromolecule #2: Decorating protein

MacromoleculeName: Decorating protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 14.867831 KDa
SequenceString:
MAQNIIAKDH QRLSNWLKEE QMGHRGLFYT RETLPVADID VKTTGSVLDS TGKLVTKATI ADATYILITD LHDYANAQMS HAVVLARGF AKIGSKAVIF GADVDDADKA TVFEAFKAKN IFAVDQIEGA FENVTFA

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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 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 12148
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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