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- PDB-9lbn: The composite cryo-EM structure of the head-to-tail connector and... -

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Basic information

Entry
Database: PDB / ID: 9lbn
TitleThe composite cryo-EM structure of the head-to-tail connector and head-proximal tail components of bacteriophage phiXacJX1
Components
  • adaptor protein gp5
  • portal protein gp1
  • stopper protein gp6
  • terminator protein gp8
  • tube protein gp9
KeywordsVIRUS / Xanthomonas phage / head-to-tail connector / tail
Biological speciesXanthomonas phage phiXacJX1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGuo, M. / Wang, A. / Zheng, Y. / Liu, C. / Shao, Q. / Fang, Q.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5


Theoretical massNumber of molelcules
Total (without water)188,8868
Polymers188,8868
Non-polymers00
Water00
1
H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5

H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5

H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5

H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5

H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5

H: portal protein gp1
I: adaptor protein gp5
J: stopper protein gp6
K: terminator protein gp8
L: tube protein gp9
M: tube protein gp9
h: portal protein gp1
i: adaptor protein gp5


Theoretical massNumber of molelcules
Total (without water)1,133,31348
Polymers1,133,31348
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein portal protein gp1


Mass: 46652.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source
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
Source: (natural) Xanthomonas phage phiXacJX1 (virus)
#2: Protein adaptor protein gp5


Mass: 12313.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source
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
Source: (natural) Xanthomonas phage phiXacJX1 (virus)
#3: Protein stopper protein gp6


Mass: 13217.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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
Source: (natural) Xanthomonas phage phiXacJX1 (virus)
#4: Protein terminator protein gp8


Mass: 13104.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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
Source: (natural) Xanthomonas phage phiXacJX1 (virus)
#5: Protein tube protein gp9


Mass: 22315.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source
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
Source: (natural) Xanthomonas phage phiXacJX1 (virus)
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: Xanthomonas phage phiXacJX1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Xanthomonas phage phiXacJX1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Xanthomonas citri pv. citri
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 26 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFIND4CTF correction
9RELION4initial Euler assignment
10RELION4final Euler assignment
12RELION43D reconstruction
13PHENIX1.19.2-4158-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 109188
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79701 / Symmetry type: POINT

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