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- PDB-8r69: Neck and tail of phage 812 virion (composite) -

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Basic information

Entry
Database: PDB / ID: 8r69
TitleNeck and tail of phage 812 virion (composite)
Components
  • (Capsid protein) x 2
  • Baseplate hub assembly protein
  • Major tail sheath protein
  • Non-cytoplasmic protein
  • Portal protein
  • Putative neck protein
  • Putative non-cytoplasmic protein
KeywordsVIRUS / phage / neck / connector / tail
Function / homology
Function and homology information


viral capsid / metal ion binding
Similarity search - Function
Phage termination protein / Bacteriophage/Gene transfer agent portal protein / Phage portal protein
Similarity search - Domain/homology
Non-cytoplasmic protein / Portal protein / Non-cytoplasmic protein / Major tail sheath protein / Neck protein / Capsid protein / Baseplate hub assembly protein / Capsid protein
Similarity search - Component
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsCienikova, Z. / Novacek, J. / Fuzik, T. / Benesik, M. / 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. / Pantucek, R. / Plevka, P.
History
DepositionNov 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Capsid protein
V: Major tail sheath protein
U: Capsid protein
W: Major tail sheath protein
A: Portal protein
B: Portal protein
E: Capsid protein
G: Baseplate hub assembly protein
N: Putative non-cytoplasmic protein
n: Putative non-cytoplasmic protein
S: Non-cytoplasmic protein
s: Non-cytoplasmic protein
C: Putative neck protein
D: Putative neck protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,51617
Polymers479,32014
Non-polymers1963
Water00
1
T: Capsid protein
V: Major tail sheath protein
U: Capsid protein
W: Major tail sheath protein
A: Portal protein
B: Portal protein
E: Capsid protein
G: Baseplate hub assembly protein
N: Putative non-cytoplasmic protein
n: Putative non-cytoplasmic protein
S: Non-cytoplasmic protein
s: Non-cytoplasmic protein
C: Putative neck protein
D: Putative neck protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)2,877,095102
Polymers2,875,91784
Non-polymers1,17718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
MethodUCSF CHIMERA

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Components

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Protein , 8 types, 14 molecules TUVWABEGNnSsCD

#1: Protein Capsid protein / Tail tube protein


Mass: 15942.970 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTP2
#2: Protein Major tail sheath protein / Tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WZ79
#3: Protein Portal protein


Mass: 64155.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WIV9
#4: Protein Capsid protein / Stopper protein


Mass: 33757.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN7
#5: Protein Baseplate hub assembly protein / Tail terminator protein


Mass: 31799.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN9
#6: Protein Putative non-cytoplasmic protein / Terminator cement protein


Mass: 10146.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WZ69
#7: Protein Non-cytoplasmic protein / Stopper cement protein


Mass: 17885.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WIM1
#8: Protein Putative neck protein / Adaptor protein


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

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Non-polymers , 1 types, 3 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: Staphylococcus phage 812 / Type: VIRUS / Details: Purified phage virion / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Details of virusEmpty: NO / 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 / Details: Purified virion particles
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: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 49 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 30553
Image scansWidth: 4000 / Height: 4000 / Movie frames/image: 16

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
4Gctf1.0.6CTF correction
7UCSF Chimera1.16model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D 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: 23947 / Details: Manual particle selection
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: OTHER / Num. of particles: 21731 / Algorithm: FOURIER SPACE
Details: This is a composite map created by merging two focused reconstructions. The composite map was then low-pass filtered to the (gold-standard cut-off 0.143) resolution of the input ...Details: This is a composite map created by merging two focused reconstructions. The composite map was then low-pass filtered to the (gold-standard cut-off 0.143) resolution of the input reconstruction with worse resolution.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18QJE

8qje

18QJE1PDBexperimental model
28QKH

8qkh

18QKH2PDBexperimental model
38R5G

8r5g

18R5G3PDBexperimental model

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