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- PDB-2hi5: Model for bacteriophage fd from cryo-EM -

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Basic information

Entry
Database: PDB / ID: 2hi5
TitleModel for bacteriophage fd from cryo-EM
ComponentsCoat protein B
KeywordsVIRUS / helix / helical VIRUS / structural protein / DNA binding protein
Function / homologyPhage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesEnterobacteria phage fd (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8 Å
AuthorsWang, Y.A. / Yu, X. / Overman, S. / Tsuboi, M. / Thomas, G.J. / Egelman, E.H.
CitationJournal: J Mol Biol / Year: 2006
Title: The structure of a filamentous bacteriophage.
Authors: Ying A Wang / Xiong Yu / Stacy Overman / Masamichi Tsuboi / George J Thomas / Edward H Egelman /
Abstract: Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure ...Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure of such filaments have depended upon techniques such as modeling or X-ray fiber diffraction, given that direct visualization of the subunit organization has not been possible. We report the first image reconstruction of a filamentous virus, bacteriophage fd, by cryoelectron microscopy. Although these thin ( approximately 70 A in diameter) rather featureless filaments scatter weakly, we have been able to achieve a nominal resolution of approximately 8 A using an iterative helical reconstruction procedure. We show that two different conformations of the virus exist, and that in both states the subunits are packed differently than in conflicting models previously proposed on the basis of X-ray fiber diffraction or solid-state NMR studies. A significant fraction of the population of wild-type fd is either disordered or in multiple conformational states, while in the presence of the Y21M mutation, this heterogeneity is greatly reduced, consistent with previous observations. These results show that new computational approaches to helical reconstruction can greatly extend the ability to visualize heterogeneous protein polymers at a reasonably high resolution.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Dec 18, 2019Group: Advisory / Other / Category: atom_sites / cell / pdbx_validate_symm_contact
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.angle_alpha / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 14, 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 / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as representative helical assembly
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Coat protein B


Theoretical massNumber of molelcules
Total (without water)5,2441
Polymers5,2441
Non-polymers00
Water0
1
A: Coat protein B
x 55


Theoretical massNumber of molelcules
Total (without water)288,42055
Polymers288,42055
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation54
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 55 / Rise per n subunits: 17.4 Å / Rotation per n subunits: -34.616 °)
Detailshelical polymer

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Components

#1: Protein/peptide Coat protein B / Major coat protein


Mass: 5244.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fd (virus) / Genus: InovirusFf phages / Species: Enterobacteria phage M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P69539

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeParent-IDDetails
1Bacteriophage fdVIRUS0
2Coat protein B1viral capsid
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1400 nm
Specimen holderSpecimen holder type: Gatan
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: IHRSR / Category: 3D reconstruction
CTF correctionDetails: phase flipping of entire images
3D reconstructionMethod: IHRSR / Resolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 16367 / Nominal pixel size: 2.4 Å / Actual pixel size: 2.4 Å / Magnification calibration: TMV
Details: The C-N bond distance is 0.09 A between GLN15 and ALA16, 0.12 A between ALA35 and THR36 and 0.44 A between ALA25 and TRP26
Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms315 0 0 0 315

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