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- PDB-9o7m: Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Ba... -

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Basic information

Entry
Database: PDB / ID: 9o7m
TitleCryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies
ComponentsYfdQ Protein
KeywordsVIRAL PROTEIN / D18 symmetry / shell-like structure / DUF2303 / YfdQ
Biological speciesCaudoviricetes (bacterial and archaeal viruses with head-tail morphology)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGuzzo, C.R. / Araujo, G.G. / Merighi, D.G.S.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
Sao Paulo Research Foundation (FAPESP)2022/08730-7 Brazil
Sao Paulo Research Foundation (FAPESP)2017/17303-7, 2021/10577-0 Brazil
Sao Paulo Research Foundation (FAPESP)2023/13894-1, 2023/16089-2 Brazil
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of YfdQ reveals a widespread family of bacteriophage-associated proteins with shell-like assemblies.
Authors: Davi Gabriel Salustiano Merighi / Guilherme Camargo Pompeu / Gabriel Guarany de Araujo / Anacleto Silva de Souza / Germán Gustavo Sgro / Chuck Shaker Farah / Cristiane Rodrigues Guzzo /
Abstract: Bacteriophages are key players in microbial ecosystems with strong biotechnological potential, yet many phage-encoded proteins remain uncharacterized. We present the structure of the YfdQ complex ...Bacteriophages are key players in microbial ecosystems with strong biotechnological potential, yet many phage-encoded proteins remain uncharacterized. We present the structure of the YfdQ complex from the Xanthomonas citri ΦXacm4-11 phage, a conserved DUF2303 protein encoded by double-stranded DNA bacteriophages of the Caudoviricetes class. Using cryo-electron microscopy, we report that native YfdQ assembles into a shell-like structure with D18 symmetry forming a ∼1.1 MegaDalton complex, a hollow interior and a unique equatorial β strand stitching oligomerization interface that holds together the two hemispheres. YfdQ homologs are widely distributed among phages infecting diverse bacterial hosts, suggesting a conserved biological role. YfdQ are found in prophages and cryptic phages. Our results suggest that heterologous expression of YfdQ in X. citri and in Escherichia coli allows the obtention of structurally heterogeneous YfdQ complexes, suggesting that its proper assembly into the shell-like structure may depend on still unidentified viral factors.
History
DepositionApr 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / 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: YfdQ Protein
D: YfdQ Protein
E: YfdQ Protein
F: YfdQ Protein
G: YfdQ Protein
H: YfdQ Protein
I: YfdQ Protein
J: YfdQ Protein
K: YfdQ Protein
L: YfdQ Protein
M: YfdQ Protein
N: YfdQ Protein
O: YfdQ Protein
P: YfdQ Protein
Q: YfdQ Protein
R: YfdQ Protein
S: YfdQ Protein
T: YfdQ Protein
U: YfdQ Protein
V: YfdQ Protein
W: YfdQ Protein
X: YfdQ Protein
Y: YfdQ Protein
Z: YfdQ Protein
a: YfdQ Protein
b: YfdQ Protein
c: YfdQ Protein
d: YfdQ Protein
e: YfdQ Protein
f: YfdQ Protein
g: YfdQ Protein
h: YfdQ Protein
i: YfdQ Protein
j: YfdQ Protein
k: YfdQ Protein
l: YfdQ Protein


Theoretical massNumber of molelcules
Total (without water)1,060,45636
Polymers1,060,45636
Non-polymers00
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 ...
YfdQ Protein


Mass: 29457.115 Da / Num. of mol.: 36 / Source method: isolated from a natural source
Source: (natural) Caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Strain: phiXacm4-11
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: YfdQ pprotein complex / Type: COMPLEX / Details: YfdQ / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.059 MDa / Experimental value: YES
Source (natural)Organism: Caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Strain: phiXacm4-11
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Xanthomonas citri pv. citri str. 306 / Strain: 306
Buffer solutionpH: 7.5
Details: 50 mM Tris-HCl, 100 mM NaCl, 10 mM MgSO47(H2O), pH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: native particles produced during phiXacm4-11 infection
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: A purified YfdQ proteins were pipetted over Glow-Discharged Quantifoil CU-R2/2 400 Mesh grids with a 2 nm ultrathin carbon layer and vitrified by plunge-freezing using a Vitrobot (Thermo ...Details: A purified YfdQ proteins were pipetted over Glow-Discharged Quantifoil CU-R2/2 400 Mesh grids with a 2 nm ultrathin carbon layer and vitrified by plunge-freezing using a Vitrobot (Thermo Fisher Scientific). The sample was drained by 3.5 s blot and 0 force, and 4.5 s and 0 force programs.

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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: 500 nm / Cs: 0.001 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 44.89 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Details: Data were acquired using a Titan Krios G3i cryo-electron microscope, 300 kV (Thermo Fisher Scientific), at the LNNano facility, CNPEM, Campinas, Brazil. The microscope was equipped with a 4k- ...Details: Data were acquired using a Titan Krios G3i cryo-electron microscope, 300 kV (Thermo Fisher Scientific), at the LNNano facility, CNPEM, Campinas, Brazil. The microscope was equipped with a 4k-4k CMOS camera, phase plate, spherical aberration corrector, and Falcon 3 detector without energy filter or a K3 detector with energy filter. For the native YfdQ dataset, data collection utilized the Falcon 3 detector in counting mode.

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
Image processingDetails: Using CryoSPARC, patch motion correction and patch CTF estimation jobs were run before using a combination of Blob Picker and Template Picker in micrograph subsets to obtain a stack of ...Details: Using CryoSPARC, patch motion correction and patch CTF estimation jobs were run before using a combination of Blob Picker and Template Picker in micrograph subsets to obtain a stack of 369,017 particles after extraction in 460-460 pixel boxes. Rounds of 2D classification were used to select the particles that contributed to the best resolved classes. The chosen 249,600 particles were used to reconstruct an ab Initio model using D18 symmetry inferred from the 2D classes (C1 did not produce shell-like models). Homogeneous refinement using this volume as input and maintaining the symmetry yielded an interpretable model at 3.85 A resolution. To assess possible heterogeneities, a 3D classification job was run (C1 symmetry, 10 classes), but no other shell configurations could be observed. A non-uniform refinement with applied D18 symmetry of the 237,960 particles from the largest class yielded the final 3.44 A resolution map.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D18 (2x18 fold dihedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237960 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00269480
ELECTRON MICROSCOPYf_angle_d0.51793960
ELECTRON MICROSCOPYf_dihedral_angle_d7.0479756
ELECTRON MICROSCOPYf_chiral_restr0.03910800
ELECTRON MICROSCOPYf_plane_restr0.00312312

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