+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41133 | ||||||||||||
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Title | Autographa californica multiple nucleopolyhedrovirus VP39 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | nucleocapsid protein VP39 / VIRAL PROTEIN | ||||||||||||
Function / homology | Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / viral capsid / structural molecule activity / Major viral capsid protein Function and homology information | ||||||||||||
Biological species | Autographa californica multiple nucleopolyhedrovirus | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Benning FMC / Chao LH | ||||||||||||
Funding support | United States, Switzerland, 3 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly. Authors: Friederike M C Benning / Simon Jenni / Coby Y Garcia / Tran H Nguyen / Xuewu Zhang / Luke H Chao / Abstract: Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which ...Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We use electron cryomicroscopy to determine a 3.2 Å helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a distinct protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism shows that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41133.map.gz | 21.6 MB | EMDB map data format | |
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Header (meta data) | emd-41133-v30.xml emd-41133.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_41133.png | 165.8 KB | ||
Filedesc metadata | emd-41133.cif.gz | 5.8 KB | ||
Others | emd_41133_half_map_1.map.gz emd_41133_half_map_2.map.gz | 140.5 MB 140.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41133 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41133 | HTTPS FTP |
-Validation report
Summary document | emd_41133_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41133_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41133_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_41133_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41133 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41133 | HTTPS FTP |
-Related structure data
Related structure data | 8tafMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41133.map.gz / Format: CCP4 / Size: 23.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41133_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41133_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Autographa californica multiple nucleopolyhedrovirus
Entire | Name: Autographa californica multiple nucleopolyhedrovirus |
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Components |
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-Supramolecule #1: Autographa californica multiple nucleopolyhedrovirus
Supramolecule | Name: Autographa californica multiple nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 307456 Sci species name: Autographa californica multiple nucleopolyhedrovirus Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Major viral capsid protein
Macromolecule | Name: Major viral capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Autographa californica multiple nucleopolyhedrovirus |
Molecular weight | Theoretical: 35.793422 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: QMRVNRCIFA SIVSFDACIT YKSPCSPDAY HDDGWFICNN HLIKRFKMSK MVLPIFDEDD NQFKMTIARH LVGNKERGIK RILIPSATN YQDVFNLNSM MQAEQLIFHL IYNNENAVNT ICDNLKYTEG FTSNTQRVIH SVYATTKSIL DTTNPNTFCS R VSRDELRF ...String: QMRVNRCIFA SIVSFDACIT YKSPCSPDAY HDDGWFICNN HLIKRFKMSK MVLPIFDEDD NQFKMTIARH LVGNKERGIK RILIPSATN YQDVFNLNSM MQAEQLIFHL IYNNENAVNT ICDNLKYTEG FTSNTQRVIH SVYATTKSIL DTTNPNTFCS R VSRDELRF FDVTNARALR GGAGDQLFNN YSGFLQNLIR RAVAPEYLQI DTEELRFRNC ATCIIDETGL VASVPDGPEL YN PIRSSDI MRSQPNRLQI RNVLKFEGDT RELDRTLSGY EEYPTYVPLF LGYQIINSEN NFLRNDFIPR ANP UniProtKB: Major viral capsid protein |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.9000000000000001 µm / Nominal defocus min: -0.4 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 43.86 Å Applied symmetry - Helical parameters - Δ&Phi: -7.16 ° Applied symmetry - Helical parameters - Axial symmetry: D14 (2x14 fold dihedral) Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4983 |
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Startup model | Type of model: INSILICO MODEL |
Final angle assignment | Type: NOT APPLICABLE |