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- EMDB-18462: Neck of phage 812 virion (C6) -

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Basic information

Entry
Database: EMDB / ID: EMD-18462
TitleNeck of phage 812 virion (C6)
Map dataNeck of phage 812 virion (C6)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Baseplate hub assembly protein
    • Protein or peptide: Putative non-cytoplasmic protein
    • Protein or peptide: Non-cytoplasmic protein
    • Protein or peptide: Putative neck protein
  • Ligand: ZINC ION
Keywordsphage / neck / portal / connector / VIRUS
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsCienikova Z / Novacek J / Fuzik T / Benesik M / Plevka P
Funding support Czech Republic, 1 items
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, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18462.png

Downloads & links

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Map

FileDownload / File: emd_18462.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeck of phage 812 virion (C6)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 480 pix.
= 518.4 Å		1.08 Å/pix.
x 480 pix.
= 518.4 Å		1.08 Å/pix.
x 480 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.08513188 - 0.14313003
Average (Standard dev.)0.00028811747 (±0.004312905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18462_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_18462_half_map_1.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_18462_half_map_2.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Staphylococcus phage 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Baseplate hub assembly protein
    • Protein or peptide: Putative non-cytoplasmic protein
    • Protein or peptide: Non-cytoplasmic protein
    • Protein or peptide: Putative neck protein
  • Ligand: ZINC ION

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: Purified phage virion / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K1-420 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: CCM 8428
Virus shellShell ID: 1 / Diameter: 1100.0 Å

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 33.757332 KDa
SequenceString: MEKPYMIGAN SNPNVINKST TYTTTTQADE QDKPKYTTRL EFDTIDMIRF INDRGIKVLW EEAYFCPCLN PDTGHPRVDC PRCHGKGIA YLPPKETIMA IQSQEKGTNQ LDIGILDTGT AIGTTQLEKR ISYRDRFTVP EVLMPQQMIY FVNKDRIKKG I PLYYDVKE ...String:
MEKPYMIGAN SNPNVINKST TYTTTTQADE QDKPKYTTRL EFDTIDMIRF INDRGIKVLW EEAYFCPCLN PDTGHPRVDC PRCHGKGIA YLPPKETIMA IQSQEKGTNQ LDIGILDTGT AIGTTQLEKR ISYRDRFTVP EVLMPQQMIY FVNKDRIKKG I PLYYDVKE ITYIATQDGT VYEEDYEIKN NRLYLNEKYE NHTVTLKILM TLRYVVSDIL KESRYQYTKF NQPKSKFENL PQ KLLLKRE DVIVLQDPYK VNDGIEEDLE IQVDDPKASA SNPSNLGGFF GGAFK

UniProtKB: Capsid protein

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Macromolecule #2: Baseplate hub assembly protein

MacromoleculeName: Baseplate hub assembly protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 31.79968 KDa
SequenceString: MAITSVDSYL LSEIKPRLNT VLENCYIIDE VLKDFDYQTR ESFKEAFCGK NAQHEVTVGF NFPKFKNNYE AHYLIQLGQG QETKNSLGS IQSSYFEATG DTLVESSTAI REDDKLVFTV SKPIGELIKV EDIEFAKYDN LQVEGNKVSF KYQTNEDYEN Y NANIIFTE ...String:
MAITSVDSYL LSEIKPRLNT VLENCYIIDE VLKDFDYQTR ESFKEAFCGK NAQHEVTVGF NFPKFKNNYE AHYLIQLGQG QETKNSLGS IQSSYFEATG DTLVESSTAI REDDKLVFTV SKPIGELIKV EDIEFAKYDN LQVEGNKVSF KYQTNEDYEN Y NANIIFTE KKNDSKGLVK GFTVEEQVTV VGLSFNVDVA RCLDAVLKMI LISMRDSIEE QQTFQLQNLS FGDIAPIIED GD SMIFGRP TIIKYTSSLD LDYTITQDIN KLTFKERKDW K

UniProtKB: Baseplate hub assembly protein

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Macromolecule #3: Putative non-cytoplasmic protein

MacromoleculeName: Putative non-cytoplasmic protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 10.146707 KDa
SequenceString:
MSIEKKEEVI AHNEVVFRSL TQGLYVKEVD IYSDVVSYTK DVDEALAMPN TINFKNSRKY KKLIMNLDLE PLNKIQKVIY ETHLEGL

UniProtKB: Non-cytoplasmic protein

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Macromolecule #4: Non-cytoplasmic protein

MacromoleculeName: Non-cytoplasmic protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 17.885197 KDa
SequenceString:
MADEISLNPI QDAKPIDDIV DIMTYLKNGK VLRVKQDNQG DILVRMSPGK HKFTEVSRDL DKESFYYKRH WVLYNVSVNS LITFDVYLD EEYSETTKVK YPKDTIVEYT REDQEKDVAM IKEILTDNNG NYFYALIGET MLFDENKLNK VKD

UniProtKB: Non-cytoplasmic protein

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Macromolecule #5: Putative neck protein

MacromoleculeName: Putative neck protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 34.191703 KDa
SequenceString: MVNSMFGGDL DPYEKSLNYE YPYHPSGNPK HIDVSEIDNL TLADYGWSPD AVKAYMFGIV VQNPDTGQPM GDEFYNHILE RAVGKAERA LDISILPDTQ HEMRDYHETE FNSYMFVHAY RKPILQVENL QLQFNGRPIY KYPANWWKVE HLAGHVQLFP T ALMQTGQS ...String:
MVNSMFGGDL DPYEKSLNYE YPYHPSGNPK HIDVSEIDNL TLADYGWSPD AVKAYMFGIV VQNPDTGQPM GDEFYNHILE RAVGKAERA LDISILPDTQ HEMRDYHETE FNSYMFVHAY RKPILQVENL QLQFNGRPIY KYPANWWKVE HLAGHVQLFP T ALMQTGQS MSYDAVFNGY PQLAGVYPPS GATFAPQMIR LEYVSGMLPR KKAGRNKPWE MPPELEQLVI KYALKEIYQV WG NLIIGAG IANKTLEVDG ITETIGTTQS AMYGGASAQI LQINEDIKEL LDGLRAYFGY NMIGL

UniProtKB: Neck protein

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
10.0 mMNaClsodium chloride
10.0 mMCaClcalcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 30553 / Average exposure time: 1.0 sec. / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFrame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization
Particle selectionNumber selected: 23947 / Details: Manual particle selection
CTF correctionSoftware - Name: Gctf (ver. 1.0.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

8203

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 21731
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Details: Particles with genome and aligned on the capsid and neck
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: in silico modelRaptorX
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: cross-correlation coefficient
Output model

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

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