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- EMDB-62948: The composite cryo-EM structure of the head-to-tail connector and... -

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Basic information

Entry
Database: EMDB / ID: EMD-62948
TitleThe composite cryo-EM structure of the head-to-tail connector and head-proximal tail components of bacteriophage phiXacJX1
Map data
Sample
  • Virus: Xanthomonas phage phiXacJX1 (virus)
    • Protein or peptide: portal protein gp1
    • Protein or peptide: adaptor protein gp5
    • Protein or peptide: stopper protein gp6
    • Protein or peptide: terminator protein gp8
    • Protein or peptide: tube protein gp9
KeywordsXanthomonas phage / head-to-tail connector / tail / VIRUS
Biological speciesXanthomonas phage phiXacJX1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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_62948.png

Downloads & links

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Map

FileDownload / File: emd_62948.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.37 Å/pix.
x 400 pix.
= 548.8 Å		1.37 Å/pix.
x 400 pix.
= 548.8 Å		1.37 Å/pix.
x 400 pix.
= 548.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-23.438337000000001 - 39.166110000000003
Average (Standard dev.)0.00096393004 (±1.0469015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 548.8 Å
α=β=γ: 90.0 °

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Supplemental data

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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: portal protein gp1
    • Protein or peptide: adaptor protein gp5
    • Protein or peptide: stopper protein gp6
    • Protein or peptide: terminator protein gp8
    • Protein or peptide: tube protein gp9

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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: portal protein gp1

MacromoleculeName: portal protein gp1 / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Molecular weightTheoretical: 46.652449 KDa
SequenceString: MSENERPGLL GRVMSAFKPK AADAVTVASF SQRDAGLYIG SRFTSDAGRE VSVQTAMSLD AVQACVKLIS QSIAAMPLYL YKKTPDGRK EAVNHPLYDL LLSAPNSSQT AFEFFECILT AMLLHGNAYV RKLMSNGKIE SLQFMHSSRL TISQDARGAY K YAYRKLDG ...String:
MSENERPGLL GRVMSAFKPK AADAVTVASF SQRDAGLYIG SRFTSDAGRE VSVQTAMSLD AVQACVKLIS QSIAAMPLYL YKKTPDGRK EAVNHPLYDL LLSAPNSSQT AFEFFECILT AMLLHGNAYV RKLMSNGKIE SLQFMHSSRL TISQDARGAY K YAYRKLDG TQIDVPSAQV WKIRGYSLDG ENGISAIQYG AQVFGTALAA ERQAGRAFTN GNLQQIYYSV AAFLTPEQRE QF SANVAQS VESGRTPVLE GGIDVKALGL NPADAQLLQS RNYSVESICR FFAVPPSMIG HASAGTTSWG SGIEAQQLAF LGL TLAPWL RRIEQSLSLD LLTPGERRQY FVDYDVTTLL RADSAARSSF YATMVNNGVM TRDECREAEG LPKLGGNASV LTVQ SAMVP LDEITNNTGA DPAAAQGTTS LDRSAQ

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Macromolecule #2: adaptor protein gp5

MacromoleculeName: adaptor protein gp5 / type: protein_or_peptide / ID: 2
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Molecular weightTheoretical: 12.313031 KDa
SequenceString:
MALTLAMVQR HLQADLIEDD ERSYVMEQLL PAARESAEMF LNRNIYSTSE ELAAAVAAGT AGQYPLVTPR AVEQAILLML GDFYRDREA TGKPVSTSAH NLLYPYRVKV GV

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Macromolecule #3: stopper protein gp6

MacromoleculeName: stopper protein gp6 / type: protein_or_peptide / ID: 3
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Molecular weightTheoretical: 13.217896 KDa
SequenceString:
MPISAGSLKT RLLAQRRTSG TDDWGAPVQG WSDLGLFSGD VKNDTGLGAI RTAAGSGLPA SIAKYSIKVR SEVIRRWSIN SADRIIGRL PFSTQEMVFS VTGVISDFAD PSMAYILVEA GADEQ

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Macromolecule #4: terminator protein gp8

MacromoleculeName: terminator protein gp8 / type: protein_or_peptide / ID: 4
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Molecular weightTheoretical: 13.10487 KDa
SequenceString:
MTYGPILKQL LSPYFSGRVF PDAAPDVPGQ DPYVIYQRVG GIPTYFTEGA LADKANARVQ LEVWSTSKQA TYEAMVHIMR SVAAAPAME PLGQPIDDYE PALRIYGSRV DISMYYNLT

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Macromolecule #5: tube protein gp9

MacromoleculeName: tube protein gp9 / type: protein_or_peptide / ID: 5
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Molecular weightTheoretical: 22.31592 KDa
SequenceString: MALTLPKGIV FGFAPITSTT SSVTGVTRAA PPVATGTMLT AGTTVLVRSN TWTGINNRIS VVDANKALQG FDTTDTTTYP GTSGPVELI TVGAFVNFTQ QGEPSTSGGD QQFWNGQLLE DRSGRQLAIP TFKNAKTLTL PLYMDTSLPW YAAAKAADAR G EPVAVRML ...String:
MALTLPKGIV FGFAPITSTT SSVTGVTRAA PPVATGTMLT AGTTVLVRSN TWTGINNRIS VVDANKALQG FDTTDTTTYP GTSGPVELI TVGAFVNFTQ QGEPSTSGGD QQFWNGQLLE DRSGRQLAIP TFKNAKTLTL PLYMDTSLPW YAAAKAADAR G EPVAVRML LPNGDASYNY GYMSFDGDAT ITANAPITNV ATFTFLSDST LVEA

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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 correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 79701
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)

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