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- PDB-9mfe: cryoEM structure of Escherichia phage YDC107 tail core -

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Basic information

Entry
Database: PDB / ID: 9mfe
TitlecryoEM structure of Escherichia phage YDC107 tail core
ComponentsMajor tail protein V
KeywordsVIRAL PROTEIN / phage tail / bacteriophage / E. coli phage / YDC107 / helical tail / VIRUS
Function / homologyLambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2 / Major tail protein V
Function and homology information
Biological speciesEscherichia phage YDC107_1 (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsKopylov, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer
Authors: Kopylov, M. / Jenkins, M.C.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major tail protein V
B: Major tail protein V
C: Major tail protein V
D: Major tail protein V
E: Major tail protein V
F: Major tail protein V


Theoretical massNumber of molelcules
Total (without water)154,1976
Polymers154,1976
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1 - 154 / Label seq-ID: 1 - 154

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4DD
d_5EE
d_6FF

NCS oper:
IDCodeMatrixVector
1given(-0.503289666827, -0.864112832307, -0.0029196416665), (0.864117764694, -0.503286803232, -0.00169777292572), (-2.34974945852E-6, -0.0033773858007, 0.999994296614)320.903611252, 86.7498118057, 0.468291956506
2given(0.500133636702, -0.865946132976, 0.00190793688889), (0.865947169715, 0.500135263335, 0.000466508668612), (-0.00135819789594, 0.00141885587195, 0.999998071071)184.728347195, -49.6292292702, 0.0066196261771
3given(0.506338673704, 0.862316570834, 0.00559277897588), (-0.862333958193, 0.506336133604, 0.0019657960946), (-0.00113668753549, -0.00581820181889, 0.99998242808)-50.557809971, 183.480447678, 0.941313026077
4given(-0.999941476332, -0.00584481540475, -0.00910395760152), (0.00582608485632, -0.999980859633, 0.0020825712519), (-0.00911595559296, 0.00202940894268, 0.999956389476)272.972100731, 269.935012432, 0.758633833045
5given(-0.501718600635, 0.865025839611, 0.00295678582156), (-0.865029074693, -0.50170760674, -0.00376527219429), (-0.00177361580305, -0.00444681279961, 0.999988540006)85.9177238593, 321.098721705, 0.838638316799

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Components

#1: Protein
Major tail protein V


Mass: 25699.557 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Residues 155 and onwards are not resolved to high resolution and are excluded from the model
Source: (natural) Escherichia phage YDC107_1 (virus) / References: UniProt: A0A2I6TC77
Has protein modificationN
Sequence detailsThe sequence corresponds to Genbank entry MCN3709170.1. There are conflicts in the sequence ...The sequence corresponds to Genbank entry MCN3709170.1. There are conflicts in the sequence annotation with Uniprot entry A0A2I6TC77 because it is not the corresponding sequence.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Escherichia phage YDC107_1 / Type: COMPLEX
Details: Tail fragments were identified in the contaminated buffer during cryoEM sample screening
Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage YDC107_1 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 300 K / Details: blot force 1 blot time 6.5 s

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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: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 17.9 ° / Axial rise/subunit: 41.77 Å / Axial symmetry: C6
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5927 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: Modelangelo / Source name: Other / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 96.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00357290
ELECTRON MICROSCOPYf_angle_d0.66639948
ELECTRON MICROSCOPYf_chiral_restr0.04281074
ELECTRON MICROSCOPYf_plane_restr0.00491302
ELECTRON MICROSCOPYf_dihedral_angle_d5.65351006
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.32084022353E-10
ens_1d_3CCELECTRON MICROSCOPYNCS constraints4.7034163706E-13
ens_1d_4CCELECTRON MICROSCOPYNCS constraints1.87349468715E-13
ens_1d_5CCELECTRON MICROSCOPYNCS constraints1.83114088329E-11
ens_1d_6CCELECTRON MICROSCOPYNCS constraints2.72203249976E-13

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