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- PDB-9m66: Cryo-EM structure of bacteriophage NF5 capsid -

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Basic information

Entry
Database: PDB / ID: 9m66
TitleCryo-EM structure of bacteriophage NF5 capsid
ComponentsGp6
KeywordsVIRAL PROTEIN / capsid / phage / Viral gene product
Function / homology:
Function and homology information
Biological speciesBrochothrix phage NF5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsPeng, Y.N. / Liu, H.R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: Structure of a Brochothrix thermosphacta becteriophage reveals the gram-positive infected siphophage cell wall adsorption
Authors: Peng, Y.N. / Liu, H.R.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gp6
B: Gp6
C: Gp6
D: Gp6
E: Gp6
F: Gp6
G: Gp6


Theoretical massNumber of molelcules
Total (without water)202,3337
Polymers202,3337
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gp6 / Major capsid protein penton


Mass: 28904.748 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Brochothrix phage NF5 (virus) / References: UniProt: D7RWD0
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: Brochothrix phage NF5 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Brochothrix phage NF5 (virus)
Details of virusEmpty: NO / 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280219 / Symmetry type: POINT
RefinementHighest resolution: 3.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214265
ELECTRON MICROSCOPYf_angle_d0.43219381
ELECTRON MICROSCOPYf_dihedral_angle_d3.731974
ELECTRON MICROSCOPYf_chiral_restr0.0412407
ELECTRON MICROSCOPYf_plane_restr0.0042478

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