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- EMDB-18912: Neck-tail junction of phage 812 virion (C6) -

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Basic information

Entry
Database: EMDB / ID: EMD-18912
TitleNeck-tail junction of phage 812 virion (C6)
Map dataNeck-tail junction of phage 812 virion (C6)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Capsid protein
    • Protein or peptide: Baseplate hub assembly protein
    • Protein or peptide: Putative non-cytoplasmic protein
    • Protein or peptide: Major tail sheath protein
    • Protein or peptide: Non-cytoplasmic protein
    • Protein or peptide: Putative neck protein
  • Ligand: ZINC ION
Keywordsphage / neck / connector / tail / VIRUS
Function / homology
Function and homology information


: / Phage termination protein
Similarity search - Domain/homology
Non-cytoplasmic protein / Non-cytoplasmic protein / Major tail sheath protein / Neck protein / Capsid protein / Baseplate hub assembly protein / Capsid protein
Similarity search - Component
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 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 / Pantucek R / Plevka P
History
DepositionNov 16, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18912.png

Downloads & links

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Map

FileDownload / File: emd_18912.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeck-tail junction of phage 812 virion (C6)
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: 0.015
Minimum - Maximum-0.06867757 - 0.12280152
Average (Standard dev.)0.00027793203 (±0.004034012)
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_18912_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_18912_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_18912_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: Capsid protein
    • Protein or peptide: Capsid protein
    • Protein or peptide: Baseplate hub assembly protein
    • Protein or peptide: Putative non-cytoplasmic protein
    • Protein or peptide: Major tail sheath protein
    • Protein or peptide: Non-cytoplasmic 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-#7 / 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: Capsid protein

MacromoleculeName: Capsid 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: 33.757332 KDa
SequenceString: MEKPYMIGAN SNPNVINKST TYTTTTQADE QDKPKYTTRL EFDTIDMIRF INDRGIKVLW EEAYFCPCLN PDTGHPRVDC PRCHGKGIA YLPPKETIMA IQSQEKGTNQ LDIGILDTGT AIGTTQLEKR ISYRDRFTVP EVLMPQQMIY FVNKDRIKKG I PLYYDVKE ...String:
MEKPYMIGAN SNPNVINKST TYTTTTQADE QDKPKYTTRL EFDTIDMIRF INDRGIKVLW EEAYFCPCLN PDTGHPRVDC PRCHGKGIA YLPPKETIMA IQSQEKGTNQ LDIGILDTGT AIGTTQLEKR ISYRDRFTVP EVLMPQQMIY FVNKDRIKKG I PLYYDVKE ITYIATQDGT VYEEDYEIKN NRLYLNEKYE NHTVTLKILM TLRYVVSDIL KESRYQYTKF NQPKSKFENL PQ KLLLKRE DVIVLQDPYK VNDGIEEDLE IQVDDPKASA SNPSNLGGFF GGAFK

UniProtKB: Capsid protein

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Macromolecule #2: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 15.94297 KDa
SequenceString:
MASEAKQTVH TGNTVLLMIK GKPVGRAQSA SGQREYGTTG VYEIGSIMPQ EHVYLRYEGT ITVERLRMKK ENFADLGYAS LGEEILKKD IIDILVVDNL TKQVIISYHG CSANNYNETW QTNEIVTEEI EFSYLTASDK ART

UniProtKB: Capsid protein

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Macromolecule #3: Baseplate hub assembly protein

MacromoleculeName: Baseplate hub assembly protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 31.79968 KDa
SequenceString: MAITSVDSYL LSEIKPRLNT VLENCYIIDE VLKDFDYQTR ESFKEAFCGK NAQHEVTVGF NFPKFKNNYE AHYLIQLGQG QETKNSLGS IQSSYFEATG DTLVESSTAI REDDKLVFTV SKPIGELIKV EDIEFAKYDN LQVEGNKVSF KYQTNEDYEN Y NANIIFTE ...String:
MAITSVDSYL LSEIKPRLNT VLENCYIIDE VLKDFDYQTR ESFKEAFCGK NAQHEVTVGF NFPKFKNNYE AHYLIQLGQG QETKNSLGS IQSSYFEATG DTLVESSTAI REDDKLVFTV SKPIGELIKV EDIEFAKYDN LQVEGNKVSF KYQTNEDYEN Y NANIIFTE KKNDSKGLVK GFTVEEQVTV VGLSFNVDVA RCLDAVLKMI LISMRDSIEE QQTFQLQNLS FGDIAPIIED GD SMIFGRP TIIKYTSSLD LDYTITQDIN KLTFKERKDW K

UniProtKB: Baseplate hub assembly protein

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Macromolecule #4: Putative non-cytoplasmic protein

MacromoleculeName: Putative non-cytoplasmic protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 10.146707 KDa
SequenceString:
MSIEKKEEVI AHNEVVFRSL TQGLYVKEVD IYSDVVSYTK DVDEALAMPN TINFKNSRKY KKLIMNLDLE PLNKIQKVIY ETHLEGL

UniProtKB: Non-cytoplasmic protein

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Macromolecule #5: Major tail sheath protein

MacromoleculeName: Major tail sheath protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 64.559008 KDa
SequenceString: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS ...String:
MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS VEHDEETQKA SRLVLKVGDQ EVKSYDLTGG AYDYTNAIIT DINQLPDFEA KLSPFGDKNL ESSKLDKIEN AN IKDKAVY VKAVFGDLEK QTAYNGIVSF EQLNAEGEVP SNVEVEAGEE SATVTATSPI KTIEPFELTK LKGGTNGEPP ATW ADKLDK FAHEGGYYIV PLSSKQSVHA EVASFVKERS DAGEPMRAIV GGGFNESKEQ LFGRQASLSN PRVSLVANSG TFVM DDGRK NHVPAYMVAV ALGGLASGLE IGESITFKPL RVSSLDQIYE SIDLDELNEN GIISIEFVRN RTNTFFRIVD DVTTF NDKS DPVKAEMAVG EANDFLVSEL KVQLEDQFIG TRTINTSASI IKDFIQSYLG RKKRDNEIQD FPAEDVQVIV EGNEAR ISM TVYPIRSFKK ISVSLVYKQQ TLQA

UniProtKB: Major tail sheath protein

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Macromolecule #6: Non-cytoplasmic protein

MacromoleculeName: Non-cytoplasmic protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 17.885197 KDa
SequenceString:
MADEISLNPI QDAKPIDDIV DIMTYLKNGK VLRVKQDNQG DILVRMSPGK HKFTEVSRDL DKESFYYKRH WVLYNVSVNS LITFDVYLD EEYSETTKVK YPKDTIVEYT REDQEKDVAM IKEILTDNNG NYFYALIGET MLFDENKLNK VKD

UniProtKB: Non-cytoplasmic protein

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Macromolecule #7: Putative neck protein

MacromoleculeName: Putative neck protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / 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 / 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
DetailsPurified virion particles

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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: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 21731
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 containing 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-8r5g:
Neck-tail junction of phage 812 virion (C6)

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