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- EMDB-18395: Portal and anchor DNA of phage 812 after tail contraction (C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-18395
TitlePortal and anchor DNA of phage 812 after tail contraction (C1)
Map dataPortal and anchor DNA of phage 812 after tail contraction (C1)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Portal protein
Keywordsphage / neck / portal / anchor DNA / VIRUS
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / viral capsid / Portal protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsCienikova Z / Siborova M / Fuzik T / Plevka P
Funding support Czech Republic, 1 items
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
DepositionSep 6, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18395.png

Downloads & links

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Map

FileDownload / File: emd_18395.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPortal and anchor DNA of phage 812 after tail contraction (C1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 405.888 Å		1.06 Å/pix.
x 384 pix.
= 405.888 Å		1.06 Å/pix.
x 384 pix.
= 405.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0067
Minimum - Maximum-0.01511062 - 0.037063595
Average (Standard dev.)0.00043721983 (±0.0020891433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 405.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18395_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_18395_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_18395_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: Portal protein

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Purified phage virion was incubated in urea and LTA to induce tail contraction and genome ejection.
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: Yes
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: CCM 8428
Virus shellShell ID: 1 / Diameter: 1100.0 Å

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Details: Dodecamer / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString: MADLFKQFRL GKDYGNNSTI AQVPIDEGLQ ANIKKIEQDN KEYQDLTKSL YGQQQAYAEP FIEMMDTNPE FRDKRSYMKN EHNLHDVLKK FGNNPILNAI ILTRSNQVAM YCQPARYSEK GLGFEVRLRD LDAEPGRKEK EEMKRIEDFI VNTGKDKDVD RDSFQTFCKK ...String:
MADLFKQFRL GKDYGNNSTI AQVPIDEGLQ ANIKKIEQDN KEYQDLTKSL YGQQQAYAEP FIEMMDTNPE FRDKRSYMKN EHNLHDVLKK FGNNPILNAI ILTRSNQVAM YCQPARYSEK GLGFEVRLRD LDAEPGRKEK EEMKRIEDFI VNTGKDKDVD RDSFQTFCKK IVRDTYIYDQ VNFEKVFNKN NKTKLEKFIA VDPSTIFYAT DKKGKIIKGG KRFVQVVDKR VVASFTSREL AMGIRNPRTE LSSSGYGLSE VEIAMKEFIA YNNTESFNDR FFSHGGTTRG ILQIRSDQQQ SQHALENFKR EWKSSLSGIN GSWQIPVVMA DDIKFVNMTP TANDMQFEKW LNYLINIISA LYGIDPAEIG FPNRGGATGS KGGSTLNEAD PGKKQQQSQN KGLQPLLRFI EDLVNRHIIS EYGDKYTFQF VGGDTKSATD KLNILKLETQ IFKTVNEARE EQGKKPIEGG DIILDASFLQ GTAQLQQDKQ YNDGKQKERL QMMMSLLEGD NDDSEEGQST DSSNDDKEIG TDAQIKGDDN VYRTQTSNKG QGRKGEKSSD FKH

UniProtKB: Portal protein

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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 / Mesh: 200 / 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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 15371 / Average exposure time: 7.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 130000
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: 32222
Details: Particle selection using cross-correlation against capsid template
Startup modelType of model: EMDB MAP
EMDB ID:

8209

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 16974
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 17304 / Software - Name: RELION (ver. 3.1)
Details: C12 reconstruction of the portal was symmetry-expanded, classified with a mask on anchor DNA without orient. search, and a class with resolved DNA ends was selected and cleaned from replicates.
FSC plot (resolution estimation)

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