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- PDB-3j5v: PhuZ201 filament -

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Basic information

Entry
Database: PDB / ID: 3j5v
TitlePhuZ201 filament
ComponentsPhuZ201 subunit
KeywordsVIRAL PROTEIN / PhuZ / tubulin / FtsZ / filament / bacteriophage / cytoskeleton / bacteriophage centering function
Function / homology
Function and homology information


establishment of localization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / GTPase activity / GTP binding / identical protein binding
Similarity search - Function
: / Phage tubulin-like protein, C-terminal domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Phage tubulin-like protein
Similarity search - Component
Biological speciesPseudomonas phage 201phi2-1 (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsZehr, E.A.
CitationJournal: Structure / Year: 2014
Title: The structure and assembly mechanism of a novel three-stranded tubulin filament that centers phage DNA.
Authors: Elena A Zehr / James A Kraemer / Marcella L Erb / Joanna K C Coker / Elizabeth A Montabana / Joe Pogliano / David A Agard /
Abstract: Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural ...Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural diversity is poorly understood. Here, we determine a 7.1 Å cryo-electron microscopy reconstruction of the bacteriophage-encoded PhuZ filament and provide molecular-level insight into its cooperative assembly mechanism. The PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating efficient phage replication. Our reconstruction and derived model reveal the first example of a three-stranded tubulin filament. We show that the elongated C-terminal tail simultaneously stabilizes both longitudinal and lateral interactions, which in turn define filament architecture. Identified interaction surfaces are conserved within the PhuZ family, and their mutagenesis compromises polymerization in vitro and in vivo. Combining kinetic modeling of PhuZ filament assembly and structural data, we suggest a common filament structure and assembly mechanism for the PhuZ family of tubulins.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Other
Revision 1.2Apr 23, 2014Group: Refinement description
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
a: PhuZ201 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5683
Polymers35,1001
Non-polymers4682
Water00
1
a: PhuZ201 subunit
hetero molecules
x 9


Theoretical massNumber of molelcules
Total (without water)320,10827
Polymers315,9009
Non-polymers4,20818
Water0
TypeNameSymmetry operationNumber
helical symmetry operation8
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: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 9 / Rise per n subunits: 14.42 Å / Rotation per n subunits: -116.44 °)

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Components

#1: Protein PhuZ201 subunit


Mass: 35100.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage 201phi2-1 (virus) / Gene: 201phi2-1p059 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: B3FK34
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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

ComponentName: PhuZ filament / Type: COMPLEX
Molecular weightValue: 0.034621 MDa / Experimental value: NO
Buffer solutionName: 250 mM KCl, 50 mM HEPES pH 7.4, 1 mM MgCl2, 10% glycerol, 1mM DTT
pH: 8
Details: 250 mM KCl, 50 mM HEPES pH 7.4, 1 mM MgCl2, 10% glycerol, 1mM DTT
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-FLAT holey carbon grid, 200 mesh copper grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 %
Details: Blotted 2 seconds before plunging in liquid ethane (FEI VITROBOT MARK III)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Nov 21, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 62000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.2 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
Image scansNum. digital images: 461

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3SPIDER3D reconstruction
CTF correctionDetails: Whole micrograph
Helical symmertyAngular rotation/subunit: -116.44 ° / Axial rise/subunit: 14.42 Å / Axial symmetry: C1
3D reconstructionMethod: Helical reconstruction / Resolution: 7.1 Å / Num. of particles: 23243 / Nominal pixel size: 1.20398 Å
Details: A modified version of SPIDER program was used for the reconstruction. Helical symmetry search was performed with hsearch_lorentz.
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation
Details: METHOD--Flexible fitting DETAILS--Flexible fitting applied to C-terminus (residues 273-315)
Atomic model buildingPDB-ID: 3R4V

3r4v


Accession code: 3R4V / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7.1 Å
Refinement stepCycle: LAST / Highest resolution: 7.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 29 0 2435

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