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- PDB-8f2m: Phi-29 scaffolding protein bound to intermediate-state MCP -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8f2m
TitlePhi-29 scaffolding protein bound to intermediate-state MCP
Components
  • Capsid assembly scaffolding protein
  • Major capsid protein
KeywordsVIRUS / bacteriophage / prohead / scaffold / HK97 fold
Function / homology
Function and homology information


viral scaffold / viral procapsid / T=3 icosahedral viral capsid / virion assembly / DNA binding
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Capsid assembly scaffolding protein / Major capsid protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWoodson, M.E. / Morais, M.C. / Jardine, P.J. / Scott, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122979 United States
CitationJournal: Sci Adv / Year: 2025
Title: Phi29 assembly intermediates reveal how scaffold interactions with capsid protein drive capsid construction and maturation
Authors: Woodson, M. / Prokhorov, N.S. / Scott, S.D. / Zhao, W. / Zhang, W. / Choi, K.H. / Jardine, P.J. / Morais, M.C.
History
DepositionNov 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Major capsid protein
F: Capsid assembly scaffolding protein
B: Capsid assembly scaffolding protein
C: Capsid assembly scaffolding protein


Theoretical massNumber of molelcules
Total (without water)83,7424
Polymers83,7424
Non-polymers00
Water00
1


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

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Components

#1: Protein Major capsid protein / Gene product 8 / gp8 / Major head protein / Protein p8


Mass: 49894.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P13849
#2: Protein Capsid assembly scaffolding protein / Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein


Mass: 11282.529 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P13848
Has protein modificationN

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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 phi29 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus phage phi29 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Bacillus subtilis
Virus shellName: capsid / Diameter: 35 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisC4H11NO31
25 mMmagnesium chlorideMgCl21
350 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5593

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.19model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 89000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034775
ELECTRON MICROSCOPYf_angle_d0.5946467
ELECTRON MICROSCOPYf_dihedral_angle_d4.62633
ELECTRON MICROSCOPYf_chiral_restr0.04746
ELECTRON MICROSCOPYf_plane_restr0.006834

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