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- PDB-6r3a: BACTERIOPHAGE SPP1 MATURE CAPSID PROTEIN -

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Basic information

Entry
Database: PDB / ID: 6r3a
TitleBACTERIOPHAGE SPP1 MATURE CAPSID PROTEIN
ComponentsMajor capsid protein
KeywordsVIRUS / Bacteriophage / Capsid protein / image processing
Function / homologyMajor capsid protein 13-like / Major capsid protein 13-like / T=7 icosahedral viral capsid / viral capsid / Major capsid protein
Function and homology information
Biological speciesBacillus phage SPP1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsIgnatiou, A. / El Sadek Fadel, M. / Buerger, J. / Mielke, T. / Topf, M. / Tavares, P.
CitationJournal: Nat Commun / Year: 2019
Title: Structural transitions during the scaffolding-driven assembly of a viral capsid.
Authors: Athanasios Ignatiou / Sandrine Brasilès / Mehdi El Sadek Fadel / Jörg Bürger / Thorsten Mielke / Maya Topf / Paulo Tavares / Elena V Orlova /
Abstract: Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid ...Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid protein (MCP) to build an icosahedral lattice. Here we report near-atomic resolution cryo-EM structures of the bacteriophage SPP1 procapsid, the intermediate expanded procapsid with partially released SPs, and the mature capsid with DNA. In the intermediate state, SPs are bound only to MCP pentons and to adjacent subunits from hexons. SP departure results in the expanded state associated with unfolding of the MCP N-terminus and straightening of E-loops. The newly formed extensive inter-capsomere bonding appears to compensate for release of SPs that clasp MCP capsomeres together. Subsequent DNA packaging instigates bending of MCP A domain loops outwards, closing the hexons central opening and creating the capsid auxiliary protein binding interface. These findings provide a molecular basis for the sequential structural rearrangements during viral capsid maturation.
History
DepositionMar 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)246,8097
Polymers246,8097
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)14,808,539420
Polymers14,808,539420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area65050 Å2
ΔGint-359 kcal/mol
Surface area193160 Å2
MethodPISA

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Components

#1: Protein
Major capsid protein / Gene product 13 / gp13


Mass: 35258.426 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPP1 (virus) / References: UniProt: Q38582

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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: Bacillus phage SPP1 / Type: VIRUS
Details: Mature assembly, icosahedral symmetry has been applied
Entity ID: all / Source: NATURAL
Molecular weightValue: 30 MDa / Experimental value: NO
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: SPP1sus70
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Bactria / Strain: Bacillus
Virus shellName: capsid / Diameter: 610 nm / Triangulation number (T number): 7
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Mature virions of the SPP1 bacteriophage
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Details: Sample preparation was screened in advance
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 X / Calibrated magnification: 31000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 nm / Cs: 2.3 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Temperature (max): 60 K / Temperature (min): 50 K
Image recordingAverage exposure time: 5 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7000
Details: Images were collected in movie mode, 25 images during 5 s
EM imaging opticsChromatic aberration corrector: none / Spherical aberration corrector: none
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN22particle selection
2Leginonimage acquisitionSuloway et al., 2005
4CTFFIND4CTF correction
7Cootmodel fitting
9IMAGIC5initial Euler assignment
10IMAGIC5final Euler assignment
11IMAGIC5classification
12IMAGIC53D reconstruction
13Cootmodel refinement
Image processingDetails: Movie frames were aligned using MOTIONCORR-2
CTF correctionDetails: Software used Imagic 5 / Type: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 200 / Details: 6000 particles were picked in total
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4500 / Algorithm: EXACT BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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