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- EMDB-18445: Neck of phage 812 virion (C12) -

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Basic information

Entry
Database: EMDB / ID: EMD-18445
TitleNeck of phage 812 virion (C12)
Map dataNeck of phage 812 virion (C12)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Putative neck protein
  • Ligand: ZINC ION
Keywordsphage / neck / portal / connector / VIRUS
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / viral capsid / Portal protein / Neck protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 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: 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 13, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18445.png

Downloads & links

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Map

FileDownload / File: emd_18445.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeck of phage 812 virion (C12)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 416 pix.
= 449.28 Å		1.08 Å/pix.
x 416 pix.
= 449.28 Å		1.08 Å/pix.
x 416 pix.
= 449.28 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: 0.023
Minimum - Maximum-0.1208581 - 0.18450569
Average (Standard dev.)0.00023706444 (±0.005559835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 449.28003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18445_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_18445_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_18445_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: 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-#2 / 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: Portal protein

MacromoleculeName: Portal 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: 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 #2: Putative neck protein

MacromoleculeName: Putative neck 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: 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 #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / 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
Startup modelType of model: EMDB MAP
EMDB ID:

8203

Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 16293
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-8qje:
Neck of phage 812 virion (C12)

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