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- PDB-8i8b: Outer shell and inner layer structures of Autographa californica ... -

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Basic information

Entry
Database: PDB / ID: 8i8b
TitleOuter shell and inner layer structures of Autographa californica multiple nucleopolyhedrovirus (AcMNPV)
Components
  • 38K
  • AcOrf-109 peptide
  • Early 49 Daa protein
  • Major viral capsid protein
  • Occlusion-derived virus envelope/capsid protein
  • P40
  • Viral capsid associated protein
KeywordsVIRAL PROTEIN / virus / capsid protein
Function / homology
Function and homology information


viral capsid / viral envelope / structural molecule activity
Similarity search - Function
Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Protein of unknown function DUF694 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Protein of unknown function (DUF705) / Nucleopolyhedrovirus capsid protein P87 / Baculovirus occlusion-derived virus envelope EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 ...Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Protein of unknown function DUF694 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Protein of unknown function (DUF705) / Nucleopolyhedrovirus capsid protein P87 / Baculovirus occlusion-derived virus envelope EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 / Baculovirus occlusion-derived virus envelope protein EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101 / HAD-superfamily phosphatase, subfamily IIIC / Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Major viral capsid protein / P40 / AcOrf-109 peptide / 38K / Occlusion-derived virus envelope/capsid protein / Viral capsid associated protein / Early 49 Daa protein
Similarity search - Component
Biological speciesAutographa californica multiple nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsJia, X. / Gao, Y. / Zhang, Q.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
W: Major viral capsid protein
X: Major viral capsid protein
Y: Major viral capsid protein
Z: Major viral capsid protein
A: Viral capsid associated protein
B: Viral capsid associated protein
C: Viral capsid associated protein
D: AcOrf-109 peptide
E: Early 49 Daa protein
F: P40
G: P40
H: Occlusion-derived virus envelope/capsid protein
I: Occlusion-derived virus envelope/capsid protein
J: 38K


Theoretical massNumber of molelcules
Total (without water)684,59414
Polymers684,59414
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 7 types, 14 molecules WXYZABCDEFGHIJ

#1: Protein
Major viral capsid protein


Mass: 38991.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N6WHR0
#2: Protein Viral capsid associated protein


Mass: 79974.469 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N7CTI8
#3: Protein AcOrf-109 peptide


Mass: 44851.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N7CRZ7
#4: Protein Early 49 Daa protein


Mass: 55480.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N7CTL8
#5: Protein P40


Mass: 41583.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N7CQX9
#6: Protein Occlusion-derived virus envelope/capsid protein


Mass: 33568.152 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N7CT36
#7: Protein 38K


Mass: 38070.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica multiple nucleopolyhedrovirus
References: UniProt: A0A0N7CSX4

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Autographa californica multiple nucleopolyhedrovirus / Type: VIRUS / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337988 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00430663
ELECTRON MICROSCOPYf_angle_d0.54941504
ELECTRON MICROSCOPYf_dihedral_angle_d11.87211453
ELECTRON MICROSCOPYf_chiral_restr0.0414637
ELECTRON MICROSCOPYf_plane_restr0.0045341

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