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- EMDB-51803: AcMNPV apical cap - composite map of the C2 plug -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51803
TitleAcMNPV apical cap - composite map of the C2 plug
Map dataAcMNPV apical cap - C2 plug composite map only
Sample
  • Virus: Autographa californica nucleopolyhedrovirus
    • Protein or peptide: Protein AC54
    • DNA: DNA (58-MER)
    • DNA: DNA (58-MER)
    • Protein or peptide: Occlusion-derived virus envelope protein E27
    • Protein or peptide: Protein C42
Keywordsnucleocapsid / VIRUS
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / virion component / viral envelope / host cell nucleus / virion membrane / membrane
Similarity search - Function
Baculovirus VP1054 / Baculovirus VP1054 protein / Baculovirus occlusion-derived virus envelope EC27 / Baculovirus occlusion-derived virus envelope protein EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101
Similarity search - Domain/homology
Protein C42 / Protein AC54 / Occlusion-derived virus envelope protein E27
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEffantin G / Kandiah E / Pelosse M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus.
Authors: Gregory Effantin / Eaazhisai Kandiah / Martin Pelosse /
Abstract: Baculoviruses are large DNA viruses found in nature propagating amongst insects and lepidoptera in particular. They have been studied for decades and are nowadays considered as invaluable ...Baculoviruses are large DNA viruses found in nature propagating amongst insects and lepidoptera in particular. They have been studied for decades and are nowadays considered as invaluable biotechnology tools used as biopesticides, recombinant expression systems or delivery vehicle for gene therapy. However, little is known about the baculovirus nucleocapsid assembly at a molecular level. Here, we solve the whole structure of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) nucleocapsid by applying cryo-electron microscopy (CryoEM) combined with de novo modelling and Alphafold predictions. Our structure completes prior observations and elucidates the intricate architecture of the apical cap, unravelling the organization of a DNA portal featuring intriguing symmetry mismatches between its core and vertex. The core, closing the capsid at the apex, holds two DNA helices of the viral genome tethered to Ac54 proteins. Different symmetry components at the apical cap and basal structure are constituted of the same building block, made of Ac101/Ac144, proving the versatility of this modular pair. The crown forming the portal vertex displays a C21 symmetry and contains, amongst others, the motor-like protein Ac66. Our findings support the viral portal to be involved in DNA packaging, probably in conjunction with other parts of a larger DNA packaging apparatus.
History
DepositionOct 11, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51803.png

Downloads & links

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Map

FileDownload / File: emd_51803.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcMNPV apical cap - C2 plug composite map only
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.007394189 - 0.02741965
Average (Standard dev.)0.00023046284 (±0.0013059438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Autographa californica nucleopolyhedrovirus

EntireName: Autographa californica nucleopolyhedrovirus
Components
  • Virus: Autographa californica nucleopolyhedrovirus
    • Protein or peptide: Protein AC54
    • DNA: DNA (58-MER)
    • DNA: DNA (58-MER)
    • Protein or peptide: Occlusion-derived virus envelope protein E27
    • Protein or peptide: Protein C42

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Supramolecule #1: Autographa californica nucleopolyhedrovirus

SupramoleculeName: Autographa californica nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 46015
Sci species name: Autographa californica nucleopolyhedrovirus
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Protein AC54

MacromoleculeName: Protein AC54 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 42.15116 KDa
SequenceString: MCSTKKPIKL DLCASVKLTP FKPMRPPKPM QCWIHPRRAN CKVTRPRNNY SDPDNENDML HMTVLNSVFL NEHAKLYYRH LLRNDQAEA RKTILNADSV YECMLIRPIR TEHFRSVDEA GEHNMSVLKI IIDAVIKYIG KLADDEYILI ADRMYVDLIY S EFRAIILP ...String:
MCSTKKPIKL DLCASVKLTP FKPMRPPKPM QCWIHPRRAN CKVTRPRNNY SDPDNENDML HMTVLNSVFL NEHAKLYYRH LLRNDQAEA RKTILNADSV YECMLIRPIR TEHFRSVDEA GEHNMSVLKI IIDAVIKYIG KLADDEYILI ADRMYVDLIY S EFRAIILP QSAYIIKGDY AESDSESGQS VDVCNELEYP WKLITANNCI VSTDESRQSQ YIYRTFLLYN TVLTAILKQN NP FDVIAEN TSISIIVRNL GSCPNNKDRV KCCDLNYGGV PPGHVMCPPR EITKKFFHYA KWVRNPNKYK RYSELIARQS ETG GGSASL RENVNNQLHA RDVSQLHLLD WENFMGEFSS YFGLHAHNV

UniProtKB: Protein AC54

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Macromolecule #4: Occlusion-derived virus envelope protein E27

MacromoleculeName: Occlusion-derived virus envelope protein E27 / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 33.568152 KDa
SequenceString: MKRIKCNKVR TVTEIVNSDE KIQKTYELAE FDLKNLSSLE SYETLKIKLA LSKYMAMLST LEMTQPLLEI FRNKADTRQI AAVVFSTLA FIHNRFHPLV TNFTNKMEFV VTETNDTSIP GEPILFTENE GVLLCSVDRP SIVKMLSREF DTEALVNFEN D NCNVRIAK ...String:
MKRIKCNKVR TVTEIVNSDE KIQKTYELAE FDLKNLSSLE SYETLKIKLA LSKYMAMLST LEMTQPLLEI FRNKADTRQI AAVVFSTLA FIHNRFHPLV TNFTNKMEFV VTETNDTSIP GEPILFTENE GVLLCSVDRP SIVKMLSREF DTEALVNFEN D NCNVRIAK TFGASKRKNT TRSDDYESNK QPNYDMDLSD FSITEVEATQ YLTLLLTVEH AYLHYYIFKN YGVFEYCKSL TD HSLFTNK LRSTMSTKTS NLLLSKFKFT IEDFDKINSN SVTSGFNIYN FNK

UniProtKB: Occlusion-derived virus envelope protein E27

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Macromolecule #5: Protein C42

MacromoleculeName: Protein C42 / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 41.583594 KDa
SequenceString: MSAIALYLEI NKLRLKIDEP MQLAIWPQLF PLLCDEHQSV QLNTDVLINF MMHVARKSQN TILNNNAAIA SQYAAGNADV VAAPASAQP TPRPVINLFA RANAAAPAQP SEELINMRRY RNAARKLIHH YSLNSTSSTE YKISDVVMTM IFLLRSEKYH S LFKLLETT ...String:
MSAIALYLEI NKLRLKIDEP MQLAIWPQLF PLLCDEHQSV QLNTDVLINF MMHVARKSQN TILNNNAAIA SQYAAGNADV VAAPASAQP TPRPVINLFA RANAAAPAQP SEELINMRRY RNAARKLIHH YSLNSTSSTE YKISDVVMTM IFLLRSEKYH S LFKLLETT FDDYTCRPQM TQVQTDTLLD AVRSLLEMPS TTIDLTTVDI MRSSFARCFN SPIMRYAKIV LLQNVALQRD KR TTLEELL IERGEKIQML QPQQYINSGT EIPFCDDAEF LNRLLKHIDP YPLSRMYYNA ANTMFYTTME NYAVSNCKFN IED YNNIFK VMENIRKHSN KNSNDQDELN IYLGVQSSNA KRKKY

UniProtKB: Protein C42

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Macromolecule #2: DNA (58-MER)

MacromoleculeName: DNA (58-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 17.953662 KDa
SequenceString: (DT)(DA)(DT)(DT)(DC)(DC)(DA)(DA)(DA)(DC) (DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DC)(DT) (DT)(DT)(DA)(DG)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DA)(DA)(DA)(DC)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DT) ...String:
(DT)(DA)(DT)(DT)(DC)(DC)(DA)(DA)(DA)(DC) (DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DC)(DT) (DT)(DT)(DA)(DG)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DA)(DA)(DA)(DC)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DT)(DT)(DT) (DA)(DA)(DT)(DT)(DA)(DA)(DA)(DT)(DG)(DG)

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Macromolecule #3: DNA (58-MER)

MacromoleculeName: DNA (58-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 17.778432 KDa
SequenceString: (DC)(DC)(DA)(DT)(DT)(DT)(DA)(DA)(DT)(DT) (DA)(DA)(DA)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DG)(DT)(DT)(DT)(DT)(DA)(DC) (DT)(DT)(DC)(DT)(DC)(DC)(DT)(DA)(DA)(DA) (DG) (DG)(DT)(DT)(DT)(DT)(DA) ...String:
(DC)(DC)(DA)(DT)(DT)(DT)(DA)(DA)(DT)(DT) (DA)(DA)(DA)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DG)(DT)(DT)(DT)(DT)(DA)(DC) (DT)(DT)(DC)(DT)(DC)(DC)(DT)(DA)(DA)(DA) (DG) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC) (DG)(DT)(DT)(DT)(DG)(DG)(DA)(DA)(DT)(DA)

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12477
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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