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- PDB-8dsp: Cryo-EM structure of the proximal half fiber in del7.3K2R1 mature... -

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Basic information

Entry
Database: PDB / ID: 8dsp
TitleCryo-EM structure of the proximal half fiber in del7.3K2R1 mature phage
ComponentsTail fiber protein
KeywordsVIRAL PROTEIN / Bacteriophage T7
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
: / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain
Similarity search - Domain/homology
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang, C. / Liu, J. / Molineux, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Asymmetric reconstruction of gp8-gp11 with terminal dsDNA associated from the del7.3K2R1.
Authors: Wang, C. / Liu, J. / Molineux, I.J.
History
DepositionJul 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Tail fiber protein
E: Tail fiber protein
F: Tail fiber protein


Theoretical massNumber of molelcules
Total (without water)55,5953
Polymers55,5953
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Tail fiber protein / Gene product 17 / Gp17 / Tail fiber protein gp17


Mass: 18531.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03748
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: Escherichia phage T7 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T7 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99318 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033951
ELECTRON MICROSCOPYf_angle_d0.4635373
ELECTRON MICROSCOPYf_dihedral_angle_d4.219547
ELECTRON MICROSCOPYf_chiral_restr0.04638
ELECTRON MICROSCOPYf_plane_restr0.003700

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