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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: 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: Image / Data content type: Image / 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 1.0Sep 11, 2024Data content type: Image / Data content type: Image / 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 1.1Feb 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
Revision 1.2Jan 21, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
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
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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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