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- PDB-9pmk: PhuZ Tubulin Tetramer from phage Goslar -

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Basic information

Entry
Database: PDB / ID: 9pmk
TitlePhuZ Tubulin Tetramer from phage Goslar
ComponentsTubulin/FtsZ GTPase domain-containing protein
KeywordsVIRAL PROTEIN / Phage / Tubulin / PhuZ
Function / homologyTubulin/FtsZ, GTPase domain superfamily / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Tubulin/FtsZ GTPase domain-containing protein
Function and homology information
Biological speciesGoslarvirus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsBasu, D. / Gu, Y. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: Structure / Year: 2026
Title: A bacteriophage tubulin forms microtubule-like assemblies with nine protofilaments.
Authors: Dwaipayan Basu / Siyu Chen / Ying-Xing Li / Niklas Klusch / Koe Inlow / Joe Pogliano / Elizabeth Villa / Kevin D Corbett /
Abstract: Tubulin family proteins play central roles in the organization and dynamics of cytoskeletal systems across the Tree of Life. In one family of bacteriophages (phages), tubulin-like proteins called ...Tubulin family proteins play central roles in the organization and dynamics of cytoskeletal systems across the Tree of Life. In one family of bacteriophages (phages), tubulin-like proteins called PhuZ (Phage tubulin/FtsZ) form dynamic filaments that position and rotate an intracellular compartment, the "phage nucleus," in which the phage genome is replicated. PhuZ filaments also mediate trafficking of nascent capsids from the cell periphery to the phage nucleus for genome packaging. PhuZ from the Pseudomonas-infecting phages 201Phi2-1 and PhiKZ form assemblies with three protofilaments. Here, we determine a 2.8 Å resolution structure of PhuZ from the E. coli-infecting phage Goslar, which forms an elaborate "cytoskeletal vortex" in infected cells. We find that in vitro-assembled Goslar PhuZ forms rigid tubes with nine nearly-straight protofilaments. The lateral interactions mediating this assembly are fundamentally different from eukaryotic tubulin, leading to a distinctive overall architecture for Goslar PhuZ filaments.
History
DepositionJul 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Tubulin/FtsZ GTPase domain-containing protein
B: Tubulin/FtsZ GTPase domain-containing protein
A: Tubulin/FtsZ GTPase domain-containing protein
D: Tubulin/FtsZ GTPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7378
Polymers142,6524
Non-polymers2,0854
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tubulin/FtsZ GTPase domain-containing protein


Mass: 35662.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal SNA tag scar / Source: (gene. exp.) Goslarvirus / Gene: Goslar_00201 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482GH76
#2: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-CPP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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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: Tubulin PhuZ from Bacteriophage Goslar / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Goslarvirus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusType: 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

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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -79.906 ° / Axial rise/subunit: 4.883 Å / Axial symmetry: C1
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14671 / Symmetry type: HELICAL
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410236
ELECTRON MICROSCOPYf_angle_d0.39613868
ELECTRON MICROSCOPYf_dihedral_angle_d10.4293836
ELECTRON MICROSCOPYf_chiral_restr0.0411540
ELECTRON MICROSCOPYf_plane_restr0.0041820

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