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- EMDB-51808: AcMNPV apical cap - C14 anchor complex only -

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Basic information

Entry
Database: EMDB / ID: EMD-51808
TitleAcMNPV apical cap - C14 anchor complex only
Map dataAcMNPV apical cap - C14 anchor complex only
Sample
  • Virus: Autographa californica nucleopolyhedrovirus
    • Protein or peptide: Occlusion-derived virus envelope protein E27
    • Protein or peptide: Protein C42
    • Protein or peptide: Protein AC142
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid-associated protein VP80
    • Protein or peptide: Protein AC109
    • Protein or peptide: Protein Ac66
    • Protein or peptide: Tyrosine-protein phosphatase
  • Ligand: ZINC ION
Keywordsnucleocapsid / VIRUS
Function / homology
Function and homology information


transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / symbiont-mediated perturbation of host cell cycle progression / nuclear capsid assembly / polynucleotide 5'-phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity ...transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / symbiont-mediated perturbation of host cell cycle progression / nuclear capsid assembly / polynucleotide 5'-phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm / viral envelope / host cell nucleus / virion membrane / structural molecule activity / protein homodimerization activity / DNA binding / membrane
Similarity search - Function
Viral desmoplakin, N-terminal / Viral Desmoplakin N-terminus / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / Baculovirus occlusion-derived virus envelope EC27 / Baculovirus occlusion-derived virus envelope protein EC27 ...Viral desmoplakin, N-terminal / Viral Desmoplakin N-terminus / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / 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 / Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / : / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Major capsid protein / Tyrosine-protein phosphatase / Protein C42 / Protein Ac66 / Protein AC109 / Protein AC142 / Occlusion-derived virus envelope protein E27 / Capsid-associated protein VP80
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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_51808.png

Downloads & links

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Map

FileDownload / File: emd_51808.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcMNPV apical cap - C14 anchor complex only
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 500 pix.
= 675. Å		1.35 Å/pix.
x 500 pix.
= 675. Å		1.35 Å/pix.
x 500 pix.
= 675. 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-0.010879954 - 0.028079493
Average (Standard dev.)0.00023525812 (±0.0014710464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 675.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51808_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AcMNPV apical cap - C14 anchor complex only - half map 1

Fileemd_51808_half_map_1.map
AnnotationAcMNPV apical cap - C14 anchor complex only - half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AcMNPV apical cap - C14 anchor complex only - half map 2

Fileemd_51808_half_map_2.map
AnnotationAcMNPV apical cap - C14 anchor complex only - half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Occlusion-derived virus envelope protein E27
    • Protein or peptide: Protein C42
    • Protein or peptide: Protein AC142
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid-associated protein VP80
    • Protein or peptide: Protein AC109
    • Protein or peptide: Protein Ac66
    • Protein or peptide: Tyrosine-protein phosphatase
  • Ligand: ZINC ION

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Supramolecule #1: Autographa californica nucleopolyhedrovirus

SupramoleculeName: Autographa californica nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / 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: Occlusion-derived virus envelope protein E27

MacromoleculeName: Occlusion-derived virus envelope protein E27 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Protein C42

MacromoleculeName: Protein C42 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: Protein AC142

MacromoleculeName: Protein AC142 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 55.480898 KDa
SequenceString: MSGGGNLLTL ERDHFKYLFL TSYFDLKDNE HVPSEPMAFI RNYLNCTFDL LDDAVLMNYF NYLQSMQLKH LVGSTSTNIF KFVKPQFRF VCDRTTVDIL EFDTRMYIKP GTPVYATNLF TSNPRKMMAF LYAEFGKVFK NKIFVNINNY GCVLAGSAGF L FDDAYVDW ...String:
MSGGGNLLTL ERDHFKYLFL TSYFDLKDNE HVPSEPMAFI RNYLNCTFDL LDDAVLMNYF NYLQSMQLKH LVGSTSTNIF KFVKPQFRF VCDRTTVDIL EFDTRMYIKP GTPVYATNLF TSNPRKMMAF LYAEFGKVFK NKIFVNINNY GCVLAGSAGF L FDDAYVDW NGVRMCAAPR LDNNMHPFRL YLLGEDMAKH FVDNNILPPH PSNAKTRKIN NSMFMLKNFY KGLPLFKSKY TV VNSTKIV TRKPNDIFNE IDKELNGNCP FIKFIQRDYI FDAQFPPDLL DLLNEYMTKS SIMKIITKFV IEENPAMSGE MSR EIILDR YSVDNYRKLY IKMEITNQFP VMYDHESSYI FVSKDFLQLK GTMNAFYAPK QRILSILAVN RLFGATETID FHPN LLVYR QSSPPVRLTG DVYVVDKNEK VFLVKHVFSN TVPAYLLIRG DYESSSDLKS LRDLNPWVQN TLLKLLIPDS VQ

UniProtKB: Protein AC142

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Macromolecule #4: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 38.991109 KDa
SequenceString: MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDDGWFICN NHLIKRFKMS KMVLPIFDED DNQFKMTIAR HLVGNKERG IKRILIPSAT NYQDVFNLNS MMQAEQLIFH LIYNNENAVN TICDNLKYTE GFTSNTQRVI HSVYATTKSI L DTTNPNTF ...String:
MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDDGWFICN NHLIKRFKMS KMVLPIFDED DNQFKMTIAR HLVGNKERG IKRILIPSAT NYQDVFNLNS MMQAEQLIFH LIYNNENAVN TICDNLKYTE GFTSNTQRVI HSVYATTKSI L DTTNPNTF CSRVSRDELR FFDVTNARAL RGGAGDQLFN NYSGFLQNLI RRAVAPEYLQ IDTEELRFRN CATCIIDETG LV ASVPDGP ELYNPIRSSD IMRSQPNRLQ IRNVLKFEGD TRELDRTLSG YEEYPTYVPL FLGYQIINSE NNFLRNDFIP RAN PNATLG GGAVAGPAPG VAGEAGGGIA V

UniProtKB: Major capsid protein

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Macromolecule #5: Capsid-associated protein VP80

MacromoleculeName: Capsid-associated protein VP80 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 79.974469 KDa
SequenceString: MNDSNSLLIT RLAAQILSRN MQTVDVIVDD KTLSLEEKID TLTSMVLAVN SPPQSPPRVT SSDLAASIIK NNSKMVGNDF EMRYNVLRM AVVFVKHYPK YYNETTAGLV AEIESNLLQY QNYVNQGNYQ NIEGYDSLLN KAEECYVKID RLFKESIKKI M DDTEAFER ...String:
MNDSNSLLIT RLAAQILSRN MQTVDVIVDD KTLSLEEKID TLTSMVLAVN SPPQSPPRVT SSDLAASIIK NNSKMVGNDF EMRYNVLRM AVVFVKHYPK YYNETTAGLV AEIESNLLQY QNYVNQGNYQ NIEGYDSLLN KAEECYVKID RLFKESIKKI M DDTEAFER EQEAERLRAE QTAANALLER RAQTSADDVV NRADANIPTA FSDPLPGPSA PRYMYESSES DTYMETARRT AE HYTDQDK DYNAAYTADE YNSLVKTVLL RLIEKALATL KNRLHITTID QLKKFRDYLN SDADAGEFQI FLNQEDCVIL KNL SNLASK FFNVRCVADT LEVMLEALRN NIELVQPESD AVRRIVIKMT QEIKDSSTPL YNIAMYKSDY DAIKNKNIKT LFDL YNDRL PINFLDTSAT SPVRKTSGKR SAEDDLLPTR SSKRANRPEI NVISSEDEQE DDDVEDVDYE KESKRRKLED EDFLK LKAL EFSKDIVNEK LQKIIVVTDG MKRLYEYCNC KNSLETLPSA ANYGSLLKRL NLYNLDHIEM NVNFYELLFP LTLYND NDN SDKTLSHQLV NYIFLASNYF QNCAKNFNYM RETFNVFGPF KQIDFMVMFV IKFNFLCDMR NFAKLIDELV PNKQPNM RI HSVLVMRDKI VKLAFSNLQF QTFSKKDKSR NTKHLQRLIM LMNANYNVI

UniProtKB: Capsid-associated protein VP80

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Macromolecule #6: Protein AC109

MacromoleculeName: Protein AC109 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 44.851441 KDa
SequenceString: MECPFQIQVC ISDRFFAFPH NLVEPQSDVG NKLIENLIVY VPTDDDRLYI DKKQFPKFNS VLVYRHEHDV NIDSRSPKKT ASATIVYWN PLVPITEIGA GETRVFSVLL TNNLFYCNTM IVHHENPKCP IEFTYPETDM QSACSALLKN RNGQSVPPPI K SNLRPIAC ...String:
MECPFQIQVC ISDRFFAFPH NLVEPQSDVG NKLIENLIVY VPTDDDRLYI DKKQFPKFNS VLVYRHEHDV NIDSRSPKKT ASATIVYWN PLVPITEIGA GETRVFSVLL TNNLFYCNTM IVHHENPKCP IEFTYPETDM QSACSALLKN RNGQSVPPPI K SNLRPIAC EIPLSHFKEL VESNDFLLCF NLETSTMVKI LSLKRIFCIF QYRKQPARYV INLPHEEIDN LYNKLNWERT RR LMKGDVP SNCATVNRSS LKYIKQAQSL LGIPDYSQTV VDFVKMFQKI IFPYQLVPNV IIKLNNFDQM VSSAPNKAEP YKK IRLFCK NDSIAISSSG IVPINMPDFS PPNTFDYSDY ANRTNINFVT QRVLTDGGFS SGITVTPVKY NYYL

UniProtKB: Protein AC109

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Macromolecule #7: Protein Ac66

MacromoleculeName: Protein Ac66 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 94.073758 KDa
SequenceString: MQRWPKYGGT DVNTRTVHDL LNTINTMSAR IKTLERYEHA LREIHKVVVI LKPSANTHSF EPDALPALIM QFLSDFAGRD INTLTHNIN YKYDYNYPPA PVPAMQPPPP PPQPPAPPQP PYYNNYPYYP PYPFSTPPPT QPPESNVAGV GGSQSLNQIT L TNEEESEL ...String:
MQRWPKYGGT DVNTRTVHDL LNTINTMSAR IKTLERYEHA LREIHKVVVI LKPSANTHSF EPDALPALIM QFLSDFAGRD INTLTHNIN YKYDYNYPPA PVPAMQPPPP PPQPPAPPQP PYYNNYPYYP PYPFSTPPPT QPPESNVAGV GGSQSLNQIT L TNEEESEL AALFKNMQTN MTWELVQNFV EVLIRIVRVH VVNNVTMINV ISSITSVRTL IDYNFTEFIR CVYQKTNIRF AI DQYLCTN IVTFIDFFTR VFYLVMRTNF QFTTFDQLTQ YSNELYTRIQ TSILQSAAPL SPPTVETVNS DIVISNLQEQ LKR ERALMQ QISEQHRIAN ERVETLQSQY DELDLKYKEI FEDKSEFAQQ KSENVRKIKQ LERSNKELND TVQKLRDENA ERLS EIQLQ KGDLDEYKNM NRQLNEDIYK LKRRIESTFD KDYVETLNDK IESLEKQLDD KQNLNRELRS SISKIDETTQ RYKLD AKDI MELKQSVSIK DQEIAMKNAQ YLELSAIYQQ TVNELTATKN ELSQVATTNQ SLFAENEESK VLLEGTLAFI DSFYQI IMQ IEKPDYVPIS KPQLTAQESI YQTDYIKDWL QKLRSKLSNA DVANLQSVSE LSDLKSQIIS IVPRNIVNRI LKENYKV KV ENVNAELLES VAVTSAVSAL VQQYERSEKQ NVKLRQEFEI KLNDLQRLLE QNQTDFESIS EFISRDPAFN RNLNDERF Q NLRQQYDEMS SKYSALETTK IKEMESIADQ AVKSEMSKLN TQLDELNSLF VKYNRKAQDI FEWKTSMLKR YETLARTTA ASVQPNVE

UniProtKB: Protein Ac66

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Macromolecule #8: Tyrosine-protein phosphatase

MacromoleculeName: Tyrosine-protein phosphatase / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-tyrosine-phosphatase
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 19.312301 KDa
SequenceString:
MFPARWHNYL QCGQVIKDSN LICFKTPLRP ELFAYVTSEE DVWTAEQIVK QNPSIGAIID LTNTSKYYDG VHFLRAGLLY KKIQVPGQT LPPESIVQEF IDTVKEFTEK CPGMLVGVHC THGINRTGYM VCRYLMHTLG IAPQEAIDRF EKARGHKIER Q NYVQDLLI

UniProtKB: Tyrosine-protein phosphatase

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 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 reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8327
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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