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Yorodumi- PDB-8i8c: Plug structure of the Autographa californica multiple nucleopolyh... -
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-Basic information
Entry | Database: PDB / ID: 8i8c | ||||||
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Title | Plug structure of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) | ||||||
Components |
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Keywords | VIRAL PROTEIN / virus / capsid protein | ||||||
Function / homology | 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 / viral envelope / P40 / Occlusion-derived virus envelope/capsid protein Function and homology information | ||||||
Biological species | Autographa californica multiple nucleopolyhedrovirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.93 Å | ||||||
Authors | Jia, X. / Gao, Y. / Zhang, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i8c.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i8c.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 8i8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i8c_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8i8c_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8i8c_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 8i8c_validation.cif.gz | 74.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i8c ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i8c | HTTPS FTP |
-Related structure data
Related structure data | 35247MC 8i8aC 8i8bC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 41583.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Autographa californica multiple nucleopolyhedrovirus References: UniProt: A0A0N7CQX9 #2: 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Autographa californica multiple nucleopolyhedrovirus / Type: VIRUS / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Autographa californica multiple nucleopolyhedrovirus |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36127 / Symmetry type: POINT |