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- EMDB-62947: Cryo-EM structure of bacteriophage phiXacJX1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-62947
TitleCryo-EM structure of bacteriophage phiXacJX1 capsid
Map data
Sample
  • Virus: Xanthomonas phage phiXacJX1 (virus)
    • Protein or peptide: major capsid protein gp3
KeywordsXanthomonas phage / capsid / icosahedron / VIRUS
Biological speciesXanthomonas phage phiXacJX1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGuo M / Wang A / Zheng Y / Liu C / Shao Q / Fang Q
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structures of a Xanthomonas phage: Insights into viral architecture and implications for the model phage HK97.
Authors: Mingcheng Guo / Aohan Wang / Yaqi Zheng / Chaoying Liu / Qianqian Shao / Yunfei Deng / Lin Li / Yueting Wang / Xiaofang Wang / Yue Shen / Jun Qian / Xiaofeng Zhou / Qianglin Fang /
Abstract: Xanthomonas bacteria are responsible for disease outbreaks in several hundred plant species, causing significant economic losses. Xanthomonas phages have emerged as a promising biocontrol strategy in ...Xanthomonas bacteria are responsible for disease outbreaks in several hundred plant species, causing significant economic losses. Xanthomonas phages have emerged as a promising biocontrol strategy in managing various important plant diseases caused by Xanthomonas bacteria. However, structural information for Xanthomonas phages has remained limited so far. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of the Xanthomonas citri phage ΦXacJX1 from siphoviruses. These structures include atomic models for the head, head-to-tail connector and head-proximal portion of the tail. ΦXacJX1's head and head-to-tail connector components show significant protein sequence and structural homology with those of the model siphophage HK97. However, the in-situ structures of head-to-tail connector of phage HK97 remain unavailable. The presented structures of phage ΦXacJX1 enhance our understanding of Xanthomonas phages and the mature virion of phage HK97. They provide a valuable framework for future structural and functional studies on both Xanthomonas phages and phage HK97.
History
DepositionJan 3, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62947.png

Downloads & links

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Map

FileDownload / File: emd_62947.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 672 pix.
= 921.984 Å		1.37 Å/pix.
x 672 pix.
= 921.984 Å		1.37 Å/pix.
x 672 pix.
= 921.984 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.032357812 - 0.053463466
Average (Standard dev.)0.00020441228 (±0.0024419022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 921.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62947_msk_1.map
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Half map: #2

Fileemd_62947_half_map_1.map
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Half map: #1

Fileemd_62947_half_map_2.map
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Sample components

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Entire : Xanthomonas phage phiXacJX1

EntireName: Xanthomonas phage phiXacJX1 (virus)
Components
  • Virus: Xanthomonas phage phiXacJX1 (virus)
    • Protein or peptide: major capsid protein gp3

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Supramolecule #1: Xanthomonas phage phiXacJX1

SupramoleculeName: Xanthomonas phage phiXacJX1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3374911 / Sci species name: Xanthomonas phage phiXacJX1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Xanthomonas citri pv. citri (bacteria)

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Macromolecule #1: major capsid protein gp3

MacromoleculeName: major capsid protein gp3 / type: protein_or_peptide / ID: 1
Details: This protein corresponds to a novel sequence that is not yet available in UniProt. The current reference for the sequence is GenBank Accession Number: PQ476032.1
Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Molecular weightTheoretical: 41.850199 KDa
SequenceString: MSDINVINST LANISDSLKA HADRAVKEQE LNASVRAKVD ELLMAQGALQ ADLKAAQQRI AEVEGNGAGG DVQHISIGQQ FVNSDSFKA MAESGGQRGR AELNIKAAIT SLTTNADGSA GATVQTTRLP GIRELPQRRM TIRSLLAQGT MEGNTLEYVR E TGFTNAAA ...String:
MSDINVINST LANISDSLKA HADRAVKEQE LNASVRAKVD ELLMAQGALQ ADLKAAQQRI AEVEGNGAGG DVQHISIGQQ FVNSDSFKA MAESGGQRGR AELNIKAAIT SLTTNADGSA GATVQTTRLP GIRELPQRRM TIRSLLAQGT MEGNTLEYVR E TGFTNAAA PVAEGAQKPE SSLKFDLVQT SAKVIAHWMK ASRQILSDSA QLQSFINARL LRGLEVVEEN QLLNGNGTGQ NL LGLLPQA TAFAAPITVA NATAVDRLRL ALLQAQLAEF PATGIVLNPA DWAGIELLKD TQGRYILGNP QGTLAPTLWG LPV VATQAM AAGQFLTGAF DAGAQVFDRW AARVEVATEN QDDFIKNMVT ILAEERLALA VYRPESFIKG SLTAAAAT

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 26.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 109188
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99189
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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