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

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Open data


ID or keywords:

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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: To Be Published
Title: Using cryogenic electron micrography methods to gain insight into structure and initial host attachment of the fagellotrophic bacteriophage 7-7-1
Authors: Noteborn, W.E.M. / Hoeksma, T. / Briegel, A.
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

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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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