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- EMDB-70204: Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Ba... -

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Entry
Database: EMDB / ID: EMD-70204
TitleCryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies
Map dataRaw map
Sample
  • Complex: YfdQ pprotein complex
    • Protein or peptide: YfdQ Protein
KeywordsD18 symmetry / shell-like structure / DUF2303 / YfdQ / VIRAL PROTEIN
Biological speciesCaudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGuzzo CR / Araujo GG / Merighi DGS
Funding support Brazil, 4 items
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, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70204.png

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Map

FileReleased
AnnotationRaw map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 460 pix.
= 395.6 Å		0.86 Å/pix.
x 460 pix.
= 395.6 Å		0.86 Å/pix.
x 460 pix.
= 395.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.422
Minimum - Maximum-0.15722173 - 0.8198009
Average (Standard dev.)0.002862633 (±0.063914165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 395.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70204_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half map

Fileemd_70204_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_70204_half_map_2.map
AnnotationHalf map
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Sample components

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Entire : YfdQ pprotein complex

EntireName: YfdQ pprotein complex
Components
  • Complex: YfdQ pprotein complex
    • Protein or peptide: YfdQ Protein

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Supramolecule #1: YfdQ pprotein complex

SupramoleculeName: YfdQ pprotein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: YfdQ
Source (natural)Organism: Caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Strain: phiXacm4-11
Molecular weightTheoretical: 1.059 MDa

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Macromolecule #1: YfdQ Protein

MacromoleculeName: YfdQ Protein / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
Strain: phiXacm4-11
Molecular weightTheoretical: 29.457115 KDa
SequenceString: MDKSAIEAIQ DSSAAAAKAT QEQIPAGITH LVAVPNGVTL QNVEISLAGR TRFRGKLVTS SIPDFVTYVK NREGGHGFID TDKLGATVF FNLGDADKPG HADHTARLTL QATPAYLAML AAGGKAFSQR DALDFIEDWS HLIGAHQVSD DGAFSPIPLA R AIAAIRKV ...String:
MDKSAIEAIQ DSSAAAAKAT QEQIPAGITH LVAVPNGVTL QNVEISLAGR TRFRGKLVTS SIPDFVTYVK NREGGHGFID TDKLGATVF FNLGDADKPG HADHTARLTL QATPAYLAML AAGGKAFSQR DALDFIEDWS HLIGAHQVSD DGAFSPIPLA R AIAAIRKV KIKAESTTEQ TEGNFQQSRS VLESVAASSD EGLPDVLSFR TEPYLGLPER TFHMRVSVST TGREPSLRFR VI ALEQEQD EIAKQFKALL LGEVGEAASM TIGTFTP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 50 mM Tris-HCl, 100 mM NaCl, 10 mM MgSO47(H2O), pH 7.5
VitrificationCryogen name: ETHANE / Chamber 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..
Detailsnative particles produced during phiXacm4-11 infection

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.89 e/Å2
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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsUsing 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 correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold 3
Final reconstructionApplied symmetry - Point group: D18 (2x18 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237960
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9o7m:
Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies

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