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- EMDB-18412: Neck of phage 812 after complete genome ejection (C12) -

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Basic information

Entry
Database: EMDB / ID: EMD-18412
TitleNeck of phage 812 after complete genome ejection (C12)
Map dataNeck of phage 812 after complete genome ejection (C12)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor protein
Keywordsphage / neck / portal / connector / VIRUS
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont entry into host cell / Portal protein / Neck protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsCienikova Z / Bardy P / 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 7, 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_18412.png

Downloads & links

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Map

FileDownload / File: emd_18412.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeck of phage 812 after complete genome ejection (C12)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 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: 0.017
Minimum - Maximum-0.0729792 - 0.09253579
Average (Standard dev.)0.00049003767 (±0.003793944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18412_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_18412_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_18412_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
    • Protein or peptide: Adaptor 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 to induce tail contraction and genome ejection, then exchanged to final buffer by centrifugation/pelleting. Vitrified particles were aggregating ...Details: Purified phage virion was incubated in urea to induce tail contraction and genome ejection, then exchanged to final buffer by centrifugation/pelleting. Vitrified particles were aggregating through their base-plates.
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: Dodecameric complex / 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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Macromolecule #2: Adaptor protein

MacromoleculeName: Adaptor protein / type: protein_or_peptide / ID: 2 / Details: Dodecameric complex / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString: MVNSMFGGDL DPYEKSLNYE YPYHPSGNPK HIDVSEIDNL TLADYGWSPD AVKAYMFGIV VQNPDTGQPM GDEFYNHILE RAVGKAERAL DISILPDTQH EMRDYHETEF NSYMFVHAYR KPILQVENLQ LQFNGRPIYK YPANWWKVEH LAGHVQLFPT ALMQTGQSMS ...String:
MVNSMFGGDL DPYEKSLNYE YPYHPSGNPK HIDVSEIDNL TLADYGWSPD AVKAYMFGIV VQNPDTGQPM GDEFYNHILE RAVGKAERAL DISILPDTQH EMRDYHETEF NSYMFVHAYR KPILQVENLQ LQFNGRPIYK YPANWWKVEH LAGHVQLFPT ALMQTGQSMS YDAVFNGYPQ LAGVYPPSGA TFAPQMIRLE YVSGMLPRKK AGRNKPWEMP PELEQLVIKY ALKEIYQVWG NLIIGAGIAN KTLEVDGITE TIGTTQSAMY GGASAQILQI NEDIKELLDG LRAYFGYNMI GL

UniProtKB: Neck 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: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified phage virion was incubated in urea to induce tail contraction and genome ejection

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Digitization - Dimensions - Width: 4000 pixel / #0 - Digitization - Dimensions - Height: 4000 pixel / #0 - Number grids imaged: 3 / #0 - Number real images: 18337 / #0 - Average exposure time: 1.0 sec. / #0 - Average electron dose: 100.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON II (4k x 4k) / #1 - Digitization - Dimensions - Width: 4000 pixel / #1 - Digitization - Dimensions - Height: 4000 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 6983 / #1 - 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

Image recording ID1
DetailsFrame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization. Data from detectors FalconII and FalconIII were merged after this step.
Particle selectionNumber selected: 8484
Details: Manual picking of non-overlapping particles with intact necks
Startup modelType of model: EMDB MAP
EMDB ID:

8209

Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: Focused reconstruction of neck sub-particle. / Number images used: 7055
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Details: Selection of classes containing empty capsids with aligned necks.
FSC plot (resolution estimation)

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