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- PDB-8qem: Neck channel of phage 812 after tail contraction (C1) -

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Basic information

Entry
Database: PDB / ID: 8qem
TitleNeck channel of phage 812 after tail contraction (C1)
Components
  • Channel DNA forward strand (63-MER)
  • Channel DNA reverse strand (63-MER)
  • Portal protein
  • Putative neck protein
KeywordsVIRUS / phage / neck / A-form DNA / connector
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / viral capsid / DNA / DNA (> 10) / Portal protein / Neck protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 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: Commun Biol / Year: 2026
Title: Genome anchoring, retention, and release by neck proteins of Staphylococcus phage 812.
Authors: Zuzana Cieniková / Jiří Nováček / Marta Šiborová / Barbora Popelářová / Tibor Füzik / Tibor Botka / Martin Benešík / Pavol Bárdy / Roman Pantůček / Pavel Plevka /
Abstract: The virion of Staphylococcus phage 812 is formed by a capsid and a contractile tail joined together by neck proteins. The neck proteins are crucial for virion assembly, DNA packaging, and the ...The virion of Staphylococcus phage 812 is formed by a capsid and a contractile tail joined together by neck proteins. The neck proteins are crucial for virion assembly, DNA packaging, and the regulation of genome release, but their functions are not completely understood. Here, we show that the neck of phage 812 consists of portal, adaptor, stopper, tail terminator, and two types of decoration proteins. A dodecameric DNA-binding site at the surface of the portal complex anchors the phage genome inside the capsid. The adaptor complex induces a local B-to-A form transition of the DNA in the neck channel that could slow or pause genome translocation during ejection. The central channel of a stopper complex that is not attached to the tail terminator complex is closed by gating loops. In contrast, in the phage 812 virion, the gating loops are in an open conformation, and the DNA extends into the tail. The structure of neck proteins is not affected by tail sheath contraction. Therefore, the expulsion of tail tape measure proteins triggers the genome release.
History
DepositionAug 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
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Revision 1.1Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative neck protein
B: Putative neck protein
C: Putative neck protein
D: Putative neck protein
E: Putative neck protein
F: Putative neck protein
G: Putative neck protein
H: Putative neck protein
I: Putative neck protein
J: Putative neck protein
K: Putative neck protein
L: Putative neck protein
M: Portal protein
N: Portal protein
O: Portal protein
P: Portal protein
Q: Portal protein
R: Portal protein
S: Portal protein
T: Portal protein
U: Portal protein
V: Portal protein
W: Portal protein
X: Portal protein
Z: Channel DNA reverse strand (63-MER)
Y: Channel DNA forward strand (63-MER)


Theoretical massNumber of molelcules
Total (without water)1,218,99526
Polymers1,218,99526
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative neck protein


Mass: 34191.703 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN6
#2: Protein
Portal protein


Mass: 64155.684 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WIV9
#3: DNA chain Channel DNA reverse strand (63-MER)


Mass: 19439.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420
#4: DNA chain Channel DNA forward strand (63-MER)


Mass: 19386.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420
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: all / 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
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.19model refinement
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: C1 (asymmetric)
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13296 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Details: B-A-B-form dsDNA model was generated with Web 3DNA 2.0. Portal and neck dodecamers were sourced from models refined in C12 symmetry. All input models were fitted into the asymmetric map. ...Details: B-A-B-form dsDNA model was generated with Web 3DNA 2.0. Portal and neck dodecamers were sourced from models refined in C12 symmetry. All input models were fitted into the asymmetric map. Tunnel loops of the portal were extended into the asymmetric density.
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails
18Q7D

8q7d

8Q7D1PDBexperimental model
2Otherin silico modelWeb 3DNA 2.0
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00472818
ELECTRON MICROSCOPYf_angle_d0.68998735
ELECTRON MICROSCOPYf_dihedral_angle_d13.02310509
ELECTRON MICROSCOPYf_chiral_restr0.04510441
ELECTRON MICROSCOPYf_plane_restr0.00812510

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