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- EMDB-35242: The helical cylinder of Autographa californica multiple nucleopol... -

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Basic information

Entry
Database: EMDB / ID: EMD-35242
TitleThe helical cylinder of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) nucleocapsid
Map datacryo-em structure of AcMNPV helical body
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: major viral capsid protein
Keywordsvirus / helical / VIRAL PROTEIN
Biological speciesAutographa californica multiple nucleopolyhedrovirus
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJia X / Gao Y / Zhang Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Architecture of the baculovirus nucleocapsid revealed by cryo-EM.
Authors: Xudong Jia / Yuanzhu Gao / Yuxuan Huang / Linjun Sun / Siduo Li / Hongmei Li / Xueqing Zhang / Yinyin Li / Jian He / Wenbi Wu / Harikanth Venkannagari / Kai Yang / Matthew L Baker / Qinfen Zhang /
Abstract: Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) has been widely used as a bioinsecticide and a protein expression vector. Despite their importance, very little is known ...Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) has been widely used as a bioinsecticide and a protein expression vector. Despite their importance, very little is known about the structure of most baculovirus proteins. Here, we show a 3.2 Å resolution structure of helical cylindrical body of the AcMNPV nucleocapsid, composed of VP39, as well as 4.3 Å resolution structures of both the head and the base of the nucleocapsid composed of over 100 protein subunits. AcMNPV VP39 demonstrates some features of the HK97-like fold and utilizes disulfide-bonds and a set of interactions at its C-termini to mediate nucleocapsid assembly and stability. At both ends of the nucleocapsid, the VP39 cylinder is constricted by an outer shell ring composed of proteins AC104, AC142 and AC109. AC101(BV/ODV-C42) and AC144(ODV-EC27) form a C14 symmetric inner layer at both capsid head and base. In the base, these proteins interact with a 7-fold symmetric capsid plug, while a portal-like structure is seen in the central portion of head. Additionally, we propose an application of AlphaFold2 for model building in intermediate resolution density.
History
DepositionFeb 3, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35242.png

Downloads & links

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Map

FileDownload / File: emd_35242.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-em structure of AcMNPV helical body
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 600 pix.
= 810. Å		1.35 Å/pix.
x 600 pix.
= 810. Å		1.35 Å/pix.
x 600 pix.
= 810. 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: 0.6
Minimum - Maximum-1.2284948 - 3.13112
Average (Standard dev.)0.011460916 (±0.10077481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 810.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35242_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_35242_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_35242_half_map_2.map
Annotationhalf map 1
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 multiple nucleopolyhedrovirus

EntireName: Autographa californica multiple nucleopolyhedrovirus
Components
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: major viral capsid protein

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Supramolecule #1: Autographa californica multiple nucleopolyhedrovirus

SupramoleculeName: Autographa californica multiple nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 307456
Sci species name: Autographa californica multiple nucleopolyhedrovirus
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: major viral capsid protein

MacromoleculeName: major viral capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
SequenceString: MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDD GWFIC NNHLIKRFKM SKMVLPIFDE DDNQFKMTIA RHLVGNKERG IKRILIPSAT NYQ DVFNLN SMMQAEQLIF HLIYNNENAV NTICDNLKYT EGFTSNTQRV IHSVYATTKS IL DTTNPNT ...String:
MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDD GWFIC NNHLIKRFKM SKMVLPIFDE DDNQFKMTIA RHLVGNKERG IKRILIPSAT NYQ DVFNLN SMMQAEQLIF HLIYNNENAV NTICDNLKYT EGFTSNTQRV IHSVYATTKS IL DTTNPNT FCSRVSRDEL RFFDVTNARA LRGGAGDQLF NNYSGFLQNL IRRAVAPEYL Q IDTEELRF RNCATCIIDE TGLVASVPDG PELYNPIRSS DIMRSQPNRL QIRNVLKFEG DTRELDRTL SGYEEYPTYV PLFLGYQIIN SENNFLRNDF IPRANPNATL GGGAVAGPA PGVAGEAGGG IAV

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 44.105 Å
Applied symmetry - Helical parameters - Δ&Phi: 18.544 °
Applied symmetry - Helical parameters - Axial symmetry: C14 (14 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58393
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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