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- PDB-8qkh: Neck of phage 812 virion (C6) -

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Basic information

Entry
Database: PDB / ID: 8qkh
TitleNeck of phage 812 virion (C6)
Components
  • Baseplate hub assembly protein
  • Capsid protein
  • Non-cytoplasmic protein
  • Putative neck protein
  • Putative non-cytoplasmic protein
KeywordsVIRUS / phage / neck / portal / connector
Function / homology: / Phage termination protein / metal ion binding / Non-cytoplasmic protein / Non-cytoplasmic protein / Neck protein / Capsid protein / Baseplate hub assembly protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 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: 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
DepositionSep 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 25, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 25, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Sep 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 25, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 25, 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
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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: 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
a: Putative neck protein
b: Putative neck protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,0709
Polymers190,0048
Non-polymers651
Water00
1
A: 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
a: Putative neck protein
b: Putative neck protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)1,140,41854
Polymers1,140,02548
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
MethodUCSF CHIMERA

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Components

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Protein , 5 types, 8 molecules AGNnSsab

#1: 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
#2: 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
#3: 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
#4: 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
#5: 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, 1 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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-#5 / 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
Specimen supportGrid material: COPPER / 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
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: 23947 / Details: Manual particle selection
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21731 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model building
ID 3D fitting-IDSource nameTypeDetails
11AlphaFoldin silico model
21Otherin silico modelRaptorX
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00475804
ELECTRON MICROSCOPYf_angle_d0.522102630
ELECTRON MICROSCOPYf_dihedral_angle_d5.0569972
ELECTRON MICROSCOPYf_chiral_restr0.04411328
ELECTRON MICROSCOPYf_plane_restr0.00413254

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