[English] 日本語
Yorodumi
- EMDB-51809: AcMNPV apical cap - C21 ring -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51809
TitleAcMNPV apical cap - C21 ring
Map dataAcMNPV apical cap - C21 ring
Sample
  • Virus: Autographa californica nucleopolyhedrovirus
    • Protein or peptide: Protein Ac66
    • Protein or peptide: Protein Ac102
    • Protein or peptide: Protein C42
Keywordsnucleocapsid / VIRUS
Function / homology
Function and homology information


virion component / host cell cytoplasm / host cell nucleus
Similarity search - Function
Baculovirus Ac102 / Baculovirus Ac102 / Viral desmoplakin, N-terminal / Viral Desmoplakin N-terminus / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101
Similarity search - Domain/homology
Protein C42 / Protein Ac66 / Protein Ac102
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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

-
Structure visualization

Supplemental images

emd_51809.png

Downloads & links

-
Map

FileDownload / File: emd_51809.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcMNPV apical cap - C21 ring
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: 0.009
Minimum - Maximum-0.018714067 - 0.039038334
Average (Standard dev.)0.00016801823 (±0.002004727)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_51809_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: AcMNPV apical cap - C21 ring -half map 2

Fileemd_51809_half_map_1.map
AnnotationAcMNPV apical cap - C21 ring -half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: AcMNPV apical cap - C21 ring - half map 1

Fileemd_51809_half_map_2.map
AnnotationAcMNPV apical cap - C21 ring - half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Autographa californica nucleopolyhedrovirus

EntireName: Autographa californica nucleopolyhedrovirus
Components
  • Virus: Autographa californica nucleopolyhedrovirus
    • Protein or peptide: Protein Ac66
    • Protein or peptide: Protein Ac102
    • Protein or peptide: Protein C42

-
Supramolecule #1: Autographa californica nucleopolyhedrovirus

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

-
Macromolecule #1: Protein Ac66

MacromoleculeName: Protein Ac66 / type: protein_or_peptide / ID: 1 / 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

-
Macromolecule #2: Protein Ac102

MacromoleculeName: Protein Ac102 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 13.345998 KDa
SequenceString:
MIASINDTDM DTDDNMSQAR RNRRNRPPAR PSAQTQMAAV DMLQTINTAA SQTAASLLIN DITPNKTESL KILSTQSVGA RSLLEPMQA NASTIKLNRI ETVNVLDFLG SVYDNTIQVI VTE

UniProtKB: Protein Ac102

-
Macromolecule #3: Protein C42

MacromoleculeName: Protein C42 / type: protein_or_peptide / ID: 3 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C21 (21 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6390
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more