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- PDB-8q7d: Neck of phage 812 after tail contraction (C12) -

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Basic information

Entry
Database: PDB / ID: 8q7d
TitleNeck of phage 812 after tail contraction (C12)
Components
  • DNA forward strand (120-MER)
  • DNA reverse strand (120-MER)
  • Portal protein
  • Putative neck protein
KeywordsVIRUS / phage / neck / portal / connector
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont entry into host cell / DNA / DNA (> 10) / DNA (> 100) / Portal protein / Neck protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsCienikova, Z. / Siborova, M. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
CitationJournal: To Be Published
Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812
Authors: Cienikova, Z. / Novacek, J. / Siborova, M. / Popelarova, B. / Fuzik, T. / Benesik, M. / Bardy, P. / Plevka, P.
History
DepositionAug 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
d: Putative neck protein
p: Portal protein
Y: DNA forward strand (120-MER)
Z: DNA reverse strand (120-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4465
Polymers172,3814
Non-polymers651
Water00
1
d: Putative neck protein
p: Portal protein
hetero molecules
x 12
Y: DNA forward strand (120-MER)
Z: DNA reverse strand (120-MER)


Theoretical massNumber of molelcules
Total (without water)1,254,98738
Polymers1,254,20226
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation11
MethodUCSF CHIMERA

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Components

#1: Protein Putative neck protein


Mass: 34191.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Adaptor protein / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN6
#2: Protein Portal protein


Mass: 64155.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WIV9
#3: DNA chain DNA forward strand (120-MER)


Mass: 36242.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420
#4: DNA chain DNA reverse strand (120-MER)


Mass: 37791.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: Staphylococcus phage 812 / Type: VIRUS
Details: Purified phage virion was incubated in urea and LTA to induce tail contraction and genome ejection
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Staphylococcus aureus / Strain: CCM 8428
Virus shellDiameter: 1100 nm
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
210 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 %

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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 magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 42 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15371
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 4000 / Height: 4000 / Movie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2SerialEMimage acquisition
4Gctf1.0.6CTF correction
7Coot0.9model fitting
9PHENIX1.19model refinement
10ISOLDE1.4model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
Image processingDetails: Frame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 32222
Details: Particle selection using cross-correlation against capsid template
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17304 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00374758
ELECTRON MICROSCOPYf_angle_d0.7101884
ELECTRON MICROSCOPYf_dihedral_angle_d7.5859144
ELECTRON MICROSCOPYf_chiral_restr0.04410824
ELECTRON MICROSCOPYf_plane_restr0.0112492

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