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- PDB-8qek: Neck and tail of phage 812 after tail contraction (composite) -

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Basic information

Entry
Database: PDB / ID: 8qek
TitleNeck and tail of phage 812 after tail contraction (composite)
Components
  • (Capsid protein) x 2
  • Anchor DNA forward strand (120-MER)
  • Anchor DNA reverse strand (120-MER)
  • Baseplate hub assembly protein
  • Major tail sheath protein
  • Portal protein
  • Putative neck protein
KeywordsVIRUS / phage / neck / tail / connector
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
DNA / DNA (> 10) / DNA (> 100) / Portal 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: 3.6 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 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_entry_details ...em_admin / pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
p: Portal protein
D: Portal protein
Y: Anchor DNA forward strand (120-MER)
Z: Anchor DNA reverse strand (120-MER)
A: Capsid protein
M: Baseplate hub assembly protein
G: Capsid protein
S: Capsid protein
b: Putative neck protein
c: Putative neck protein
B: Major tail sheath protein
I: Major tail sheath protein
O: Major tail sheath protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,04516
Polymers561,84813
Non-polymers1963
Water00
1
p: Portal protein
D: Portal protein
Y: Anchor DNA forward strand (120-MER)
Z: Anchor DNA reverse strand (120-MER)
A: Capsid protein
M: Baseplate hub assembly protein
G: Capsid protein
S: Capsid protein
b: Putative neck protein
c: Putative neck protein
B: Major tail sheath protein
I: Major tail sheath protein
O: Major tail sheath protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)3,372,26796
Polymers3,371,09078
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 , 6 types, 11 molecules pDAGMSbcBIO

#1: 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


Mass: 15942.970 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Tail tube protein / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTP2
#5: Protein Baseplate hub assembly protein


Mass: 31799.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Tail terminator protein / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN9
#6: Protein Capsid protein / Putative neck protein


Mass: 33757.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Stopper protein / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN7
#7: Protein Putative neck protein


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


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

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DNA chain , 2 types, 2 molecules YZ

#2: DNA chain Anchor DNA forward strand (120-MER)


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


Mass: 37791.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Random sequence / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420

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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 was incubated in urea and LTA to induce tail contraction and genome ejection
Entity ID: #1-#8 / 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
IDNameVersionCategoryDetails
1Gautomatch0.56particle selection
2SerialEMimage acquisition
4Gctf1.0.6CTF correction
7UCSF Chimera1.16model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13UCSF Chimera1.163D reconstructionvop maximum
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
3D reconstructionResolution: 3.6 Å / Resolution method: OTHER / Num. of particles: 17304
Details: Composite map created by merging three reconstructions and low-pass filtered to the resolution of the worst-resolved input reconstruction. The resolutions of the input maps were determined ...Details: Composite map created by merging three reconstructions and low-pass filtered to the resolution of the worst-resolved input reconstruction. The resolutions of the input maps were determined by gold-standard FSC at 0.143.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18Q7D

8q7d

18Q7D1PDBexperimental model
28Q01

8q01

18Q012PDBexperimental model
38Q1I

8q1i

18Q1I3PDBexperimental model

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