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- PDB-9hz8: Agrobacterium phage 7-7-1 capsid -

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Basic information

Entry
Database: PDB / ID: 9hz8
TitleAgrobacterium phage 7-7-1 capsid
Components
  • (Structural protein) x 3
  • Major capsid protein
KeywordsVIRAL PROTEIN / Flagella phage / Agrobacterium sp. H13-3 / Capsid
Function / homology: / Phage capsid / Phage capsid family / virion component / Structural protein / Structural protein / Major capsid protein / Structural protein
Function and homology information
Biological speciesAgrobacterium phage 7-7-1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNoteborn, W.E.M. / Hoeksma, T. / Rouchen, O.Y. / Briegel, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionJan 13, 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
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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
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Structural protein
H: Structural protein
I: Structural protein
J: Structural protein
K: Structural protein
L: Structural protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Z: Structural protein
a: Structural protein
b: Structural protein
c: Structural protein
d: Structural protein
Y: Structural protein
k: Major capsid protein
l: Major capsid protein
m: Major capsid protein
u: Major capsid protein
o: Major capsid protein
z: Structural protein
1: Structural protein
2: Structural protein
3: Structural protein
4: Structural protein
5: Structural protein
6: Structural protein
7: Structural protein
8: Structural protein
9: Structural protein
0: Structural protein
AA: Structural protein
AB: Structural protein
D: Major capsid protein
p: Structural protein
q: Structural protein
r: Structural protein
s: Structural protein
t: Structural protein
M: Structural protein
N: Structural protein
O: Structural protein
P: Structural protein
Q: Structural protein
R: Structural protein
e: Structural protein
f: Structural protein
g: Structural protein
h: Structural protein
i: Structural protein
j: Structural protein
n: Structural protein
v: Structural protein
w: Structural protein
x: Structural protein
y: Structural protein


Theoretical massNumber of molelcules
Total (without water)1,476,57264
Polymers1,476,57264
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

#1: Protein
Major capsid protein


Mass: 52592.863 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7F9G3
#2: Protein ...
Structural protein


Mass: 14286.115 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7FAS3
#3: Protein
Structural protein


Mass: 23077.988 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7F8Z7
#4: Protein/peptide
Structural protein


Mass: 3209.962 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage 7-7-1 (virus) / References: UniProt: J7F8Z6
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: all / 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 material: COPPER / Grid type: Quantifoil
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: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6975 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002676341
ELECTRON MICROSCOPYf_angle_d0.4597104007
ELECTRON MICROSCOPYf_chiral_restr0.043111268
ELECTRON MICROSCOPYf_plane_restr0.003913869
ELECTRON MICROSCOPYf_dihedral_angle_d4.531710345

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