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- EMDB-74065: The cryo-EM structure of Pakpunavirus P7-1 triplex protein and sh... -

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Basic information

Entry
Database: EMDB / ID: EMD-74065
TitleThe cryo-EM structure of Pakpunavirus P7-1 triplex protein and sheath in contracted state
Map data
Sample
  • Virus: Pakpunavirus
    • Protein or peptide: gp88
    • Protein or peptide: gp89
    • Protein or peptide: gp76
KeywordsPakpunavirus P7-1 / Cryo-EM / in situ / structure / baseplate / spike / hub / triplex / VIRAL PROTEIN
Biological speciesPakpunavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 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
Authors: Li F / Cingolani G
History
DepositionNov 25, 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_74065.png

Downloads & links

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Map

FileDownload / File: emd_74065.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 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: 0.00709
Minimum - Maximum-0.009135524 - 0.022474779
Average (Standard dev.)0.0002530022 (±0.0018671189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74065_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_74065_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: gp88
    • Protein or peptide: gp89
    • Protein or peptide: gp76

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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: gp88

MacromoleculeName: gp88 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 52.425945 KDa
SequenceString: MAGITAEGLT IKDLDQILTD YRNVASQVFA DLVSTGDEVD TSGNSALGRL IGVVAPSDEA IWEVIQMVYN SFNPAAATGV ALDNLVSFS AISRHAARPT RAQVVLEGNI NTVINSPPAK MISSSTGRVF HLLQGVILTP KACSGVGIFP QTVGNDLTYE L KMYVDDIN ...String:
MAGITAEGLT IKDLDQILTD YRNVASQVFA DLVSTGDEVD TSGNSALGRL IGVVAPSDEA IWEVIQMVYN SFNPAAATGV ALDNLVSFS AISRHAARPT RAQVVLEGNI NTVINSPPAK MISSSTGRVF HLLQGVILTP KACSGVGIFP QTVGNDLTYE L KMYVDDIN TTSIKYTSPA TGTVTSESIL AGLAADVATN HGNTLTSYEQ NGILFIVPID PFNTKTFEEA SNLSIQKVRK LG IAVDDVI GPVPQQALAI DTISIPIAGW DSVINPVPAI TGRLRETDDE LRERFRNSKF VQATNILESL IDGLMNVEGV EDV RIIEND TDNPDPVHGV PGHSFLPIVL GGIPTEVAQS IWLNKPFGIG SVGDTEVQVV DSRGYTHRVN YQRPVEVPIE IKIS VTNTG SMPENIEDIL RPRIVAYGTE NYKIGDDVIY SRFYAPIMEI PGFQVNSLTI AKKGQTQGMA NIEIGFKEVA TFAAA DITV TTV

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Macromolecule #2: gp89

MacromoleculeName: gp89 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 26.698064 KDa
SequenceString: MAVNQFDRED YLEVARERVT EQFKEKPIFD RFLQVLLSGK FDIQNALEDL QTLRSLDTAT GKQLDIIGDI VGRPRGLVYQ DIFNYFGFA GTERAGSFGS LSDPTVGAPW YSVGAPTGNA REPSDEEYRM ILKAKIIKNR TNSTPEQVIE AYKFVFGVPE V FLEEYAPA ...String:
MAVNQFDRED YLEVARERVT EQFKEKPIFD RFLQVLLSGK FDIQNALEDL QTLRSLDTAT GKQLDIIGDI VGRPRGLVYQ DIFNYFGFA GTERAGSFGS LSDPTVGAPW YSVGAPTGNA REPSDEEYRM ILKAKIIKNR TNSTPEQVIE AYKFVFGVPE V FLEEYAPA AVRIGIGKIL TNVERSLLFD LGGAGALLPK TIGVNYTYTE FQAGRVFATE GFPGGQGVGD LNDPTVGGIL TN LVT

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Macromolecule #3: gp76

MacromoleculeName: gp76 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 46.365898 KDa
SequenceString: MTVLTDVIDI QISRETAAVA QTNFNVPLFI ASHTNFSERA RVYNSLKGVA EDFGESDPTY LAAVRYFGQA LKPRSLVIGR RQVPSATVS VSVVQEGQSY VLTVNGLPVS YVSQQDDTAT LIATGLKAAY DVTPVAGVTV TDNEDGTLTV ASNEDWSLKV S SNLTMAAA ...String:
MTVLTDVIDI QISRETAAVA QTNFNVPLFI ASHTNFSERA RVYNSLKGVA EDFGESDPTY LAAVRYFGQA LKPRSLVIGR RQVPSATVS VSVVQEGQSY VLTVNGLPVS YVSQQDDTAT LIATGLKAAY DVTPVAGVTV TDNEDGTLTV ASNEDWSLKV S SNLTMAAA PSTEGWPAAI TAVQGENDEW YALSIDSHAD DDIMAVATHI EGTKKVFIGA TAQANTKTSA ENDIASRLVA AG FQRTALI YHPNADAQFP ECAWVGYQLQ EQPGSNTWTH KALAAVDAYR LTPTESTNLK NKNVTTFERV GGVNRTFGGA MAG GEWIDV MIFVDWLEAR MTERLWFRMA NSKKIPYDAV GATILESEIR AQLNEGIRVG GLAEAPAPKV FVPDVLSMSP NMRA QRIFE GIEFEARLAG AIHFVHIRGT VTV

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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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 7832
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE

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