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- EMDB-18516: Tail channel of phage 812 virion (C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-18516
TitleTail channel of phage 812 virion (C1)
Map dataTail channel of phage 812 virion (C1)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tape measure protein
Keywordsphage / neck / tail / genome / VIRUS
Function / homologyPhage tail lysozyme / Phage tail lysozyme / Major tail sheath protein / Phage tail lysozyme domain-containing protein / Capsid protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.64 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 27, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18516.png

Downloads & links

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Map

FileDownload / File: emd_18516.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail channel of phage 812 virion (C1)
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: 0.011
Minimum - Maximum-0.04067662 - 0.05533145
Average (Standard dev.)0.000716759 (±0.00327566)
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_18516_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_18516_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_18516_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: Tail tube protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tape measure 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 / 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: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString:
MASEAKQTVH TGNTVLLMIK GKPVGRAQSA SGQREYGTTG VYEIGSIMPQ EHVYLRYEGT ITVERLRMKK ENFADLGYAS LGEEILKKDI IDILVVDNLT KQVIISYHGC SANNYNETWQ TNEIVTEEIE FSYLTASDKA RT

UniProtKB: Capsid protein

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Macromolecule #2: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILAM RIEDAKPASA EIGGLKITSK IYGNVANNIQ VGLEKNTLSD SLRLRVIFQD DRFNEVYDNI GNIFTIKYKG EEANATFSVE ...String:
MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILAM RIEDAKPASA EIGGLKITSK IYGNVANNIQ VGLEKNTLSD SLRLRVIFQD DRFNEVYDNI GNIFTIKYKG EEANATFSVE HDEETQKASR LVLKVGDQEV KSYDLTGGAY DYTNAIITDI NQLPDFEAKL SPFGDKNLES SKLDKIENAN IKDKAVYVKA VFGDLEKQTA YNGIVSFEQL NAEGEVPSNV EVEAGEESAT VTATSPIKTI EPFELTKLKG GTNGEPPATW ADKLDKFAHE GGYYIVPLSS KQSVHAEVAS FVKERSDAGE PMRAIVGGGF NESKEQLFGR QASLSNPRVS LVANSGTFVM DDGRKNHVPA YMVAVALGGL ASGLEIGESI TFKPLRVSSL DQIYESIDLD ELNENGIISI EFVRNRTNTF FRIVDDVTTF NDKSDPVKAE MAVGEANDFL VSELKVQLED QFIGTRTINT SASIIKDFIQ SYLGRKKRDN EIQDFPAEDV QVIVEGNEAR ISMTVYPIRS FKKISVSLVY KQQTLQA

UniProtKB: Major tail sheath protein

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Macromolecule #3: Tail tape measure protein

MacromoleculeName: Tail tape measure protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString: MAMNDDYRLV LSGDSSDLEN SLKAIELYMD SLESKNIDAP LDNFLKKLKV IAKEVKNVQN AMDKQDGKSV ISSKDMDESI KSTQSATKNI NELKKALDDL QKENISKGIA PDPEVEKAYA KMGKVVDETQ EKLEKMSSQK IGSDASIQNR IKEMKTLNQV TEEYNKISKD ...String:
MAMNDDYRLV LSGDSSDLEN SLKAIELYMD SLESKNIDAP LDNFLKKLKV IAKEVKNVQN AMDKQDGKSV ISSKDMDESI KSTQSATKNI NELKKALDDL QKENISKGIA PDPEVEKAYA KMGKVVDETQ EKLEKMSSQK IGSDASIQNR IKEMKTLNQV TEEYNKISKD SSATKDYTKR LRANRNMTRG YMERSEGTGR LTYDQGARVR SELGKVSSYE SQRKQNQRNL EQAREQYSNY RNQQQDLTKR RASGQINKAQ YEQELASIKQ EMKAREELIS NYEKLGAELD KTVQYYKGSV QKDFQSRDVD QQRGTFGRMV QERLPSIGSH AMMGTTAMAT GLYMKGASLS ETNRPMVTSL GQNSDNMDID SVRNAYGDLS IDNKLGYNST DMLKMATSYE ASVGHKSDED TMAGTKQLAI GGRSLGIKDQ EAYQESMGQI MHTGGVNSDN MKEMQDAFLG GIKQSGMVGR QDEQLKALGS IAEQSGEGRT LTKDQMSNLT AMQSTFAESG SKGLQGEQGA NAINSIDQGL KNGMNSSYAR IAMGWGTQYQ GLEGGYDLQK RMDEGISNPE NLTDMADIAT QMGGSEKEQK YLFNRSMKEI GANLTMEQSD EIFKDSKEGK LSKEELAKKA KKMEKEGKKE GEDNATDYKE SKSGKNDQNK SKTDDKAEDT YDMAQPLRDA HSALAGLPAP IYLAIGAIGA FTASLIASAS QFGAGHLIGK GAKGLRNKFG RNKGGSSGGN PMAGGMPSGG GSPKGGGSPK GGGTRSTGGK ILDSAKGLGG FLVGGAGWKG MFGGESKGKG FKQTSKEAWS GTRKVFNRDN GRKAMDKSKD IAKGTGSGLK DIYNDSIFGK ERRQNLGEKA KGFGGKAKGL YGKFADKFGD GGKNGILSQS PKAGGSGIGK LGKLAGGLGK GAGVLGVATS ALSLIPALAS GDSKAIGGGI GSMGGGMAGA SAGASIGALF GGVGAIPGAL IGGAIGSFGG GAVGEKVGDM AKKANTKEGW NLGWTNGDKD GKNKFQDSLL GKPISKAWSG ITGLFDNDAE ASEEDSKDKK KGVKGVKGDT KKKEKMTAEQ LREKNNQSET KNLKIYSDLL DRAQKIIESA KGINIDGGTS DSGSDSGGSA SDVGGEGAEK MYKFLKGKGL SDNQVGAVMG NLQQESNLDP NAKNASSGAF GIAQWLGARK TGLENFAKSK GKKSSDMDVQ LDYLWKEMQS DYESNNLKNA GWSKGGSLEQ NTKAFATGFE RMGANEAMMG TRVNNAKEFK KKYGGSGGGG GGGALSSTYQ EAMSNPVLTT GSNYRGSNDA SNASTTNRIT VNVNVQGGNN PEETGDIIGG RIREVLDSNM DIFANEHKRS Y

UniProtKB: Phage tail lysozyme domain-containing 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
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 9102
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: 3 / Avg.num./class: 13126 / Software - Name: RELION (ver. 3.1)
Details: Neck/tail junction reconstructed in C6 was symmetry expanded to C3 then classified with a focused mask on the tail tube channel, without orientation search. Particles from the best class ...Details: Neck/tail junction reconstructed in C6 was symmetry expanded to C3 then classified with a focused mask on the tail tube channel, without orientation search. Particles from the best class were again symmetry expanded to C1 and classified with a focused mask on the tail tube channel.
FSC plot (resolution estimation)

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