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- EMDB-73999: The cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:col... -

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Basic information

Entry
Database: EMDB / ID: EMD-73999
TitleThe cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:collar:gateway)
Map data
Sample
  • Complex: Pakpunavirus
    • Protein or peptide: Portal protein
    • Protein or peptide: Tail completion protein
    • Protein or peptide: Head-tail joining protein
    • Protein or peptide: Head to Tail protein gp72
KeywordsPakpunavirus P7-1 / Cryo-EM / in situ / structure / neck / portal protein / H-t-T / collar protein / gateway protein / VIRAL PROTEIN
Biological speciesPakpunavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 neck (portal:H-t-T:collar:gateway)
Authors: Li F / Cingolani G
History
DepositionNov 21, 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_73999.png

Downloads & links

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Map

FileDownload / File: emd_73999.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 544.8 Å		1.36 Å/pix.
x 400 pix.
= 544.8 Å		1.36 Å/pix.
x 400 pix.
= 544.8 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: 0.012
Minimum - Maximum-0.025514308 - 0.050745368
Average (Standard dev.)0.00002141691 (±0.004099853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73999_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_73999_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
  • Complex: Pakpunavirus
    • Protein or peptide: Portal protein
    • Protein or peptide: Tail completion protein
    • Protein or peptide: Head-tail joining protein
    • Protein or peptide: Head to Tail protein gp72

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Supramolecule #1: Pakpunavirus

SupramoleculeName: Pakpunavirus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #4, #3, #2
Source (natural)Organism: Pakpunavirus

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 54.362641 KDa
SequenceString: MAETEKTAPG IPRLRLGEIG STGLKQVNGT ILEERRPELR FPRACRTFQM MAEDPTIKSA LDLFEMMMSR VDWEVDLGVD PDEAMKARG KFLKECMHDM EHSWYSFIKE VTSFYTYGFS VHEMVFKRRE GYPVSKYNDN KFGIKKLPIR SQSTITKWLY S EDGRNFLG ...String:
MAETEKTAPG IPRLRLGEIG STGLKQVNGT ILEERRPELR FPRACRTFQM MAEDPTIKSA LDLFEMMMSR VDWEVDLGVD PDEAMKARG KFLKECMHDM EHSWYSFIKE VTSFYTYGFS VHEMVFKRRE GYPVSKYNDN KFGIKKLPIR SQSTITKWLY S EDGRNFLG CEQSLANVVN GDRYVNLGNK DGTVEIPAKK MLLFRVDAKR DSPEGNSPLR ACYNAWRYRV EIEEQESVGV TR DMNGMPT LYLPPRYMSE DATEAERAVY EYYKRVIRNI QMNEQSGLIL PQAFDPESRQ PLFKFELTSS QGSKMYDTDA IIR RWDNKI LQALFADMLK MGQDQVGSYS LAGAKTNIMA MAIESRLREI KDVLDNKLIP TLFALNGDYS PDLPKLQYGE LDEI DLEEF SKGIQRIGSV GGLERDREVY NKIRKALKIK PRPDDEPVDV DNIMGGQSQA GKAGVGNGAS TSAAGRDNAA ANNA

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Macromolecule #2: Head to Tail protein gp72

MacromoleculeName: Head to Tail protein gp72 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 18.142607 KDa
SequenceString:
MAYTGDPANN PIDRLREIVG DVWEPPMLSD ETYQWVLDKN EGNERRAALE LMRMMLFRLT RGMRERTGDI EVYGAEYFNN YLKALQLIL KDPNIAISLA VPYAGGISKS DMLANDLDPD NVTREFYIGF ARREKLYNQC NPGPQDLSMG CDYLGKLQF

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Macromolecule #3: Head-tail joining protein

MacromoleculeName: Head-tail joining protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 14.369471 KDa
SequenceString:
MLYPTFSMTN FVKLDLIRRG QPGDDGFGRP TPPVETVVTI TANVQPIEKS TDTRILPEAD RSKACFKVYS RGEEIRQLKE GPGGWSADR FMWEGELYEV MKVINYSMGI LNHYKAICMR VERNSTA

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Macromolecule #4: Tail completion protein

MacromoleculeName: Tail completion protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 21.305135 KDa
SequenceString:
MIHTELENSL YLMVKELFPD WRVIQAYTNN QEPQTPYLAI DIKRLDELGR ENVSNMSDPI SPSHGTIQVQ QDFAAKVVFE LIGKYGETA SVSDMAMAIT RAMRTPAGHA AQRKFNLSLF KLPSTRRVPM LRETDMYMFY QVTCEFGFSV IETTTQEFAA G ADIHGVYY DAGRPGHIIE SHIDINFEH

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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 10400
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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