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- EMDB-35245: Cryo-EM structure of the major capsid protein VP39 of Autographa ... -

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Basic information

Entry
Database: EMDB / ID: EMD-35245
TitleCryo-EM structure of the major capsid protein VP39 of Autographa californica multiple nucleopolyhedrovirus (AcMNPV)
Map dataCryo-EM structure of AcMNPV VP39
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major viral capsid protein
Keywordsvirus / capsid protein / VIRAL PROTEIN
Function / homologyBaculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / viral capsid / structural molecule activity / Major viral capsid protein
Function and homology information
Biological speciesAutographa californica multiple nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsJia X / 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) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35245.png

Downloads & links

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Map

FileDownload / File: emd_35245.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of AcMNPV VP39
Projections & slices

Image control

Size
Brightness
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.8512588 - 4.31769
Average (Standard dev.)0.0010896575 (±0.033804867)
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_35245_msk_1.map
Projections & Slices
AxesZYX

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Half map: half map 1

Fileemd_35245_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_35245_half_map_2.map
Annotationhalf map 2
Projections & Slices
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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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple 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 viral capsid protein

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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

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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1635004
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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