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- EMDB-18372: Neck channel of phage 812 after tail contraction (C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-18372
TitleNeck channel of phage 812 after tail contraction (C1)
Map dataNeck channel of phage 812 after tail contraction (C1)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Putative neck protein
    • Protein or peptide: Portal protein
    • DNA: Channel DNA reverse strand (63-MER)
    • DNA: Channel DNA forward strand (63-MER)
Keywordsphage / neck / A-form DNA / 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: 3.96 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
DepositionAug 31, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18372.png

Downloads & links

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Map

FileDownload / File: emd_18372.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeck channel 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 416 pix.
= 439.712 Å		1.06 Å/pix.
x 416 pix.
= 439.712 Å		1.06 Å/pix.
x 416 pix.
= 439.712 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: 0.011
Minimum - Maximum-0.01860386 - 0.041595794
Average (Standard dev.)0.0003767884 (±0.002027256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 439.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18372_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_18372_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_18372_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: Putative neck protein
    • Protein or peptide: Portal protein
    • DNA: Channel DNA reverse strand (63-MER)
    • DNA: Channel DNA forward strand (63-MER)

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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: Putative neck protein

MacromoleculeName: Putative neck protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / 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 #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 64.155684 KDa
SequenceString: MADLFKQFRL GKDYGNNSTI AQVPIDEGLQ ANIKKIEQDN KEYQDLTKSL YGQQQAYAEP FIEMMDTNPE FRDKRSYMKN EHNLHDVLK KFGNNPILNA IILTRSNQVA MYCQPARYSE KGLGFEVRLR DLDAEPGRKE KEEMKRIEDF IVNTGKDKDV D RDSFQTFC ...String:
MADLFKQFRL GKDYGNNSTI AQVPIDEGLQ ANIKKIEQDN KEYQDLTKSL YGQQQAYAEP FIEMMDTNPE FRDKRSYMKN EHNLHDVLK KFGNNPILNA IILTRSNQVA MYCQPARYSE KGLGFEVRLR DLDAEPGRKE KEEMKRIEDF IVNTGKDKDV D RDSFQTFC KKIVRDTYIY DQVNFEKVFN KNNKTKLEKF IAVDPSTIFY ATDKKGKIIK GGKRFVQVVD KRVVASFTSR EL AMGIRNP RTELSSSGYG LSEVEIAMKE FIAYNNTESF NDRFFSHGGT TRGILQIRSD QQQSQHALEN FKREWKSSLS GIN GSWQIP VVMADDIKFV NMTPTANDMQ FEKWLNYLIN IISALYGIDP AEIGFPNRGG ATGSKGGSTL NEADPGKKQQ QSQN KGLQP LLRFIEDLVN RHIISEYGDK YTFQFVGGDT KSATDKLNIL KLETQIFKTV NEAREEQGKK PIEGGDIILD ASFLQ GTAQ LQQDKQYNDG KQKERLQMMM SLLEGDNDDS EEGQSTDSSN DDKEIGTDAQ IKGDDNVYRT QTSNKGQGRK GEKSSD FKH

UniProtKB: Portal protein

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Macromolecule #3: Channel DNA reverse strand (63-MER)

MacromoleculeName: Channel DNA reverse strand (63-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 19.439512 KDa
SequenceString: (DG)(DA)(DT)(DA)(DG)(DA)(DA)(DT)(DT)(DA) (DT)(DT)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DT) (DT)(DG)(DT)(DC)(DT)(DT)(DC)(DT)(DA) (DA)(DT)(DC)(DT)(DA)(DC)(DT)(DC)(DT)(DC) (DA) (DG)(DT)(DA)(DG)(DT)(DA) ...String:
(DG)(DA)(DT)(DA)(DG)(DA)(DA)(DT)(DT)(DA) (DT)(DT)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DT) (DT)(DG)(DT)(DC)(DT)(DT)(DC)(DT)(DA) (DA)(DT)(DC)(DT)(DA)(DC)(DT)(DC)(DT)(DC) (DA) (DG)(DT)(DA)(DG)(DT)(DA)(DG)(DT) (DA)(DA)(DT)(DA)(DG)(DT)(DA)(DG)(DT)(DA) (DC)(DA) (DT)(DA)(DA)

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Macromolecule #4: Channel DNA forward strand (63-MER)

MacromoleculeName: Channel DNA forward strand (63-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 19.386502 KDa
SequenceString: (DT)(DT)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DA) (DC)(DT)(DA)(DT)(DT)(DA)(DC)(DT)(DA)(DC) (DT)(DA)(DC)(DT)(DG)(DA)(DG)(DA)(DG) (DT)(DA)(DG)(DA)(DT)(DT)(DA)(DG)(DA)(DA) (DG) (DA)(DC)(DA)(DA)(DC)(DG) ...String:
(DT)(DT)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DA) (DC)(DT)(DA)(DT)(DT)(DA)(DC)(DT)(DA)(DC) (DT)(DA)(DC)(DT)(DG)(DA)(DG)(DA)(DG) (DT)(DA)(DG)(DA)(DT)(DT)(DA)(DG)(DA)(DA) (DG) (DA)(DC)(DA)(DA)(DC)(DG)(DG)(DT) (DA)(DC)(DC)(DA)(DA)(DT)(DA)(DA)(DT)(DT) (DC)(DT) (DA)(DT)(DC)

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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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 13296
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: Neck aligned in C6 was symmetry-expanded to C1 and classified with a mask on the channel DNA without orientation search
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8q7d

source_name: PDB, initial_model_type: experimental model
source_name: Other, initial_model_type: in silico modelWeb 3DNA 2.0
DetailsB-A-B-form dsDNA model was generated with Web 3DNA 2.0. Portal and neck dodecamers were sourced from models refined in C12 symmetry. All input models were fitted into the asymmetric map. Tunnel loops of the portal were extended into the asymmetric density.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model

PDB-8qem:
Neck channel of phage 812 after tail contraction (C1)

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