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- PDB-9rku: Agrobacterium phage 7-7-1 baseplate -

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Basic information

Entry
Database: PDB / ID: 9rku
TitleAgrobacterium phage 7-7-1 baseplate
Components
  • (Baseplate protein) x 2
  • (Putative tail biosynthetic ...) x 2
  • (Structural protein) x 2
  • Putative structural protein
  • Tail sheath protein
KeywordsVIRUS / Flagella phage / Agrobacterium sp. H13-3 / Baseplate
Function / homology
Function and homology information


Bacteriophage Mu, Baseplate protein gp46 / Phage protein GP46 / DNA circulation, N-terminal / DNA circularisation protein N-terminus / Baseplate protein J-like / Baseplate J-like protein barrel domain
Similarity search - Domain/homology
Baseplate protein / Structural protein / Putative tail biosynthetic protein / Putative structural protein / Tail sheath protein / Putative tail biosynthetic protein / Structural protein / Baseplate protein
Similarity search - Component
Biological speciesAgrobacterium phage 7-7-1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsNoteborn, W.E.M. / Hoeksma, T. / Briegel, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: Commun Biol / Year: 2025
Title: Insights into the structure and initial host attachment of the flagellotropic bacteriophage 7-7-1.
Authors: W E M Noteborn / R Ouyang / T Hoeksma / A Sidi Mabrouk / N C Esteves / D M Pelt / B E Scharf / A Briegel /
Abstract: Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. ...Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. Using single particle analysis (SPA) cryo-electron microscopy (cryo-EM), we determined the capsid, neck region, tail, and baseplate complex structures. Combined with cryo-electron tomography (cryo-ET) and machine learning methodologies, our findings indicate that phage 7-7-1 uses capsid fibers to establish initial contact with the host flagellum, followed by subsequent attachment to cell surface receptors. The study also demonstrated that capsid fibers are flexible and can interact with other phages and host flagella, suggesting a cooperative infection strategy. These results provide crucial structural insights and may open avenues for developing phage-based therapeutics against resistant bacterial pathogens.
History
DepositionJun 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jan 21, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.2Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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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
Ac: Baseplate protein
Ad: Baseplate protein
Ae: Baseplate protein
Af: Putative tail biosynthetic protein
Ag: Putative tail biosynthetic protein
Ah: Putative tail biosynthetic protein
Ai: Structural protein
Aj: Structural protein
Ak: Structural protein
Al: Structural protein
Am: Structural protein
An: Structural protein
Ao: Baseplate protein
Ap: Baseplate protein
Aq: Baseplate protein
Ar: Baseplate protein
As: Baseplate protein
At: Baseplate protein
Au: Baseplate protein
Av: Baseplate protein
Aw: Baseplate protein
Ax: Baseplate protein
Ay: Baseplate protein
Az: Baseplate protein
A1: Putative tail biosynthetic protein
A2: Putative tail biosynthetic protein
A3: Putative tail biosynthetic protein
A4: Putative tail biosynthetic protein
A5: Putative tail biosynthetic protein
A6: Putative tail biosynthetic protein
A7: Putative structural protein
A8: Putative structural protein
A9: Putative structural protein
A0: Putative structural protein
BA: Putative structural protein
BB: Putative structural protein
BN: Tail sheath protein
BO: Structural protein
BC: Tail sheath protein
BP: Structural protein
BD: Tail sheath protein
BQ: Structural protein
BE: Tail sheath protein
BR: Structural protein
BF: Tail sheath protein
BS: Structural protein
BG: Tail sheath protein
BT: Structural protein
BH: Tail sheath protein
BU: Structural protein
BI: Tail sheath protein
BV: Structural protein
BJ: Tail sheath protein
BW: Structural protein
BK: Tail sheath protein
BX: Structural protein
BL: Tail sheath protein
BY: Structural protein
BM: Tail sheath protein
BZ: Structural protein


Theoretical massNumber of molelcules
Total (without water)2,122,37760
Polymers2,122,37760
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

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Protein , 6 types, 51 molecules AcAdAeAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzA7A8A9A0BABBBNBCBD...

#1: Protein Baseplate protein


Mass: 20893.727 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FAQ1
#3: Protein
Structural protein


Mass: 31473.984 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FAD9
#4: Protein
Baseplate protein


Mass: 43428.816 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7F8X4
#6: Protein
Putative structural protein


Mass: 19321.740 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FA56
#7: Protein
Tail sheath protein


Mass: 54120.355 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FA80
#8: Protein
Structural protein / Tail tube protein


Mass: 14503.347 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7F8Z8

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Putative tail biosynthetic ... , 2 types, 9 molecules AfAgAhA1A2A3A4A5A6

#2: Protein Putative tail biosynthetic protein


Mass: 49304.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7F9D2
#5: Protein
Putative tail biosynthetic protein


Mass: 43729.598 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FAD8

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Details

Has protein modificationY

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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: Agrobacterium phage 7-7-1 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / 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: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8161 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 85.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0021147342
ELECTRON MICROSCOPYf_angle_d0.4225200811
ELECTRON MICROSCOPYf_chiral_restr0.041422878
ELECTRON MICROSCOPYf_plane_restr0.002726571
ELECTRON MICROSCOPYf_dihedral_angle_d4.166420370

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