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- PDB-8i1t: The asymmetric unit of P22 empty capsid -

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Basic information

Entry
Database: PDB / ID: 8i1t
TitleThe asymmetric unit of P22 empty capsid
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / Complex / VIRUS
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXiao, H. / Liu, H.R. / Cheng, L.P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Viruses / Year: 2023
Title: Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures.
Authors: Hao Xiao / Junquan Zhou / Fan Yang / Zheng Liu / Jingdong Song / Wenyuan Chen / Hongrong Liu / Lingpeng Cheng /
Abstract: The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid ...The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation.
History
DepositionJan 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Major capsid protein
A: Major capsid protein
C: Major capsid protein
E: Major capsid protein
F: Major capsid protein
B: Major capsid protein
D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)327,5697
Polymers327,5697
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major capsid protein / Gene product 5 / gp5 / Major head protein


Mass: 46795.613 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26747

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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: Salmonella phage P22 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella phage P22 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 2400 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 406980 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00723345
ELECTRON MICROSCOPYf_angle_d0.66131745
ELECTRON MICROSCOPYf_dihedral_angle_d5.7333206
ELECTRON MICROSCOPYf_chiral_restr0.0493668
ELECTRON MICROSCOPYf_plane_restr0.0054186

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