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- EMDB-74057: The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74057
TitleThe cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status
Map data
Sample
  • Virus: Pakpunavirus
    • Protein or peptide: gp88
    • Protein or peptide: gp89
    • Protein or peptide: gp83
    • Protein or peptide: gp79
    • Protein or peptide: gp78
    • Protein or peptide: gp84
    • Protein or peptide: gp87
    • Protein or peptide: gp86
    • Protein or peptide: gp85
    • Protein or peptide: gp88
KeywordsPakpunavirus P7-1 / Cryo-EM / in situ / structure / baseplate / 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 baseplate in extended status
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_74057.png

Downloads & links

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Map

FileDownload / File: emd_74057.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.)
1.36 Å/pix.
x 512 pix.
= 697.344 Å		1.36 Å/pix.
x 512 pix.
= 697.344 Å		1.36 Å/pix.
x 512 pix.
= 697.344 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: 0.016
Minimum - Maximum-0.045123834 - 0.08543433
Average (Standard dev.)-0.0001810757 (±0.004486905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 697.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: masked 3d refinement using Relion

Fileemd_74057_half_map_1.map
Annotationmasked 3d refinement using Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: masked 3d refinement using Relion

Fileemd_74057_half_map_2.map
Annotationmasked 3d refinement using Relion
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: gp83
    • Protein or peptide: gp79
    • Protein or peptide: gp78
    • Protein or peptide: gp84
    • Protein or peptide: gp87
    • Protein or peptide: gp86
    • Protein or peptide: gp85
    • Protein or peptide: gp88

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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: gp83

MacromoleculeName: gp83 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 28.575006 KDa
SequenceString: MTIAIKRENG DLIWFDAVTE FGRQYRGSVS SNPIETGGKI TDHITTENPV FTLTAVVSDA DFNLNRPVIN DNEAQTYKIN NKEFVNTQP VTIPAVISTS RLDPSRIFPE VITQFIPPEI PSATVLPQKG DKVAYDIERQ LIDMQRNAEV FSLLDFRDGI I WDQIERCI ...String:
MTIAIKRENG DLIWFDAVTE FGRQYRGSVS SNPIETGGKI TDHITTENPV FTLTAVVSDA DFNLNRPVIN DNEAQTYKIN NKEFVNTQP VTIPAVISTS RLDPSRIFPE VITQFIPPEI PSATVLPQKG DKVAYDIERQ LIDMQRNAEV FSLLDFRDGI I WDQIERCI FTDLSFTENA ETGSSLQPRM TIEAVTFTDT RYVEVRVNKG RKTAKKEKRD TKEGDTGASN ATSQDSPTFK RS QMKEAQI RTQVAR

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Macromolecule #4: gp79

MacromoleculeName: gp79 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 17.714852 KDa
SequenceString:
MANTVLTYSP SDVKIVLCGY ALTGVVSFEM SWLSRPYTMV RGIRGHHTRV FNRDLSAQIR IEVLQTSVSN DAFFSLVEQD RRTQSARIT LSVKDTHGST MMSTDNAYVN GYPSITFTDG IENRVWTIDV LDWTDGTVGG NQQVGFDVFG TVQGALSYLR

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Macromolecule #5: gp78

MacromoleculeName: gp78 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 18.265016 KDa
SequenceString:
MITTYSPRDV VVTLAGIHSV TGYAEGEFIR IVKDIKPFIK HGSMDGEIAR VYNKDQGWRV ELTIMQSSPT NDILSMLYNV DIATRMGKF PLMIKDTKGS TSFLALTAWV EDLPRVSFSG QLETRTWILG CSEVAMNIGG NVDQSLVEQA ILLGSSLLPA L TQFGGF

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Macromolecule #6: gp84

MacromoleculeName: gp84 / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 14.001813 KDa
SequenceString:
MSTTYIDTLP LYQDRKYRYA VAIEGISRVL QFYWNSRSRQ WHMDIFDEEL NPILTGLAVV PQYPIMADYA MQHIGFNGYF LLMPVNLEQ VQYKHDASDI VPQFFELLYV NVDLEDDVE

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Macromolecule #7: gp87

MacromoleculeName: gp87 / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 14.19622 KDa
SequenceString:
MDLFVNPDTH DLVFINGEAP VTQRMVDIVA QRLKIKLYTF LGEWFLDDRI GIPYFERILG KSRSLPAVDA IFQSEIMRDP GVLEITSWQ SGIDPHTREY SMEFTVRTTD NTESLPITFR MIGV

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Macromolecule #8: gp86

MacromoleculeName: gp86 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 26.712225 KDa
SequenceString: MRRTGLQELL NLHSSTEGSK QYTAIPCVVL RVLDDFRRLS VDVRPVVNDL YKDGTSEEQP EILSVPVIMP GTANTLISFP LNVGDTVLC VFSQRTMDVF KGSATGQPHT PNDLRKFNMA DAIAIPGLFT FPRSMNDPAR HSWPHDTKDL TIAHNLMTGQ E AEVRIKAN ...String:
MRRTGLQELL NLHSSTEGSK QYTAIPCVVL RVLDDFRRLS VDVRPVVNDL YKDGTSEEQP EILSVPVIMP GTANTLISFP LNVGDTVLC VFSQRTMDVF KGSATGQPHT PNDLRKFNMA DAIAIPGLFT FPRSMNDPAR HSWPHDTKDL TIAHNLMTGQ E AEVRIKAN GDILINSRKT ISINAQNVNV KCASLTVDAA HTTWNGNIAH TGNYVQTGGT STFNGIPFHT HKHGGVMPGG GV TAVPQA

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Macromolecule #9: gp85

MacromoleculeName: gp85 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 33.881938 KDa
SequenceString: MKQYDRVYKL TLGNTESGQG VEITNLHPDG SLNREGLQFR FDISKSSDNK KSGNSATVEI YNLSIATLNI LETEYLTCRL EVGYKEMGT SVVLDGNVVE TSTRKSGNDY VTQLILGEGY TALTETKLKG TVSPGKTVKD VIEEIRLQMP GVDRGAYTGL N CNNPIMYG ...String:
MKQYDRVYKL TLGNTESGQG VEITNLHPDG SLNREGLQFR FDISKSSDNK KSGNSATVEI YNLSIATLNI LETEYLTCRL EVGYKEMGT SVVLDGNVVE TSTRKSGNDY VTQLILGEGY TALTETKLKG TVSPGKTVKD VIEEIRLQMP GVDRGAYTGL N CNNPIMYG YQLRGLAKDA LNSVCEANNI EWNISGNVLN VTDVNGPTTK SVQMAPLVNR ETGLIDIPFY ASASGTAQKK DQ RRRRGVQ FKCLLNPELT PGVLVRVESD RLSGTFRINN VRISGGYRDN EWYTECWCSD LNQEDIDQ

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Macromolecule #10: gp88

MacromoleculeName: gp88 / type: protein_or_peptide / ID: 10 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pakpunavirus
Molecular weightTheoretical: 86.017289 KDa
SequenceString: MITERIAQLT GELKFTVDSR PLTAFDKKLA GVEARLREFS KLTNKRFGVK LTLDTKTLRE ELAKAATQRV VLKNIAVDAA AVRLISEKL QERLNATPIR LKSVRLDLSG IRDQKNFVKT ALGQTKVDLP VELGLAQASR TLYEWKKRTE SRFKIHLNAD I SRSKLLQN ...String:
MITERIAQLT GELKFTVDSR PLTAFDKKLA GVEARLREFS KLTNKRFGVK LTLDTKTLRE ELAKAATQRV VLKNIAVDAA AVRLISEKL QERLNATPIR LKSVRLDLSG IRDQKNFVKT ALGQTKVDLP VELGLAQASR TLYEWKKRTE SRFKIHLNAD I SRSKLLQN ARNTLRDVQG RLNGLAVATP QIRLSVDRAH LRREIQDVLE QIRREVRIRI DLESSIRGGG AGGSRGTAGH IR QGMGMGI GSELAGWGRG FIPGLGGAFA IMQLNRANQE LQGQRLAMQA VGGGVQGGQE LQATLRDISQ RLGLDDRAIG SSY VKMMAA GQASNFDKTQ VDGIFQSMAE YGRVMGLDGE AMKGSFRAVE QMMGKGQIMS EELKGQLAER FPAAVALMAK SQDM TIAEL MKTMEKGELK SDALIPFART LAEEARKGGA LDAAMQGTAA QQGRFQFGWN RTIEAFAAGG FDRGMSDFFK IAAQG MKEA LPLVTALGGG FEALMRPVNA LVGIGGELGS QWENIAKQFN MTGTGLTLTT AQTLALLTPM GRLISAISWG ALALED FIV FLEGGDSVFG DFLNNNVQAA ETFEKLASES SELKNNLDGI FSVVPGLAEA LKGLEFNEML VSTMRELAAI MEFFNSV VE RFAIAGKYRD AKIAEAGGDR STIMSNIDTM YAMFNPEDAK DKATFIGDRL VAQNIDAIQT ETHTRATQSL TPDQFGYM M QRGQVRNEME GALKKSAIDI SFNLNVSGID AQGNVMTTEA QERVREIVSN VLEEEISRAS ASYKESQ

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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: 7
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 opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 10400
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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