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- EMDB-18369: Neck and tail of phage 812 after tail contraction (composite) -

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Basic information

Entry
Database: EMDB / ID: EMD-18369
TitleNeck and tail of phage 812 after tail contraction (composite)
Map dataNeck and tail of phage 812 after tail contraction (composite)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Portal protein
    • DNA: Anchor DNA forward strand (120-MER)
    • DNA: Anchor DNA reverse strand (120-MER)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Baseplate hub assembly protein
    • Protein or peptide: Capsid protein
    • Protein or peptide: Putative neck protein
    • Protein or peptide: Major tail sheath protein
  • Ligand: ZINC ION
Keywordsphage / neck / tail / connector / VIRUS
Function / homology
Function and homology information


viral capsid / metal ion binding
Similarity search - Function
: / Phage termination protein / Bacteriophage/Gene transfer agent portal protein / Phage portal protein
Similarity search - Domain/homology
Portal 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: 3.6 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-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18369.png

Downloads & links

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Map

FileDownload / File: emd_18369.map.gz / Format: CCP4 / Size: 164.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeck and tail of phage 812 after tail contraction (composite)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 520 pix.
= 549.64 Å		1.06 Å/pix.
x 288 pix.
= 304.416 Å		1.06 Å/pix.
x 288 pix.
= 304.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-4.104822 - 15.41316
Average (Standard dev.)0.000000006913734 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288520
Spacing288288520
CellA: 304.41602 Å / B: 304.41602 Å / C: 549.64 Å
α=β=γ: 90.0 °

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Supplemental data

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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
    • DNA: Anchor DNA forward strand (120-MER)
    • DNA: Anchor DNA reverse strand (120-MER)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Baseplate hub assembly protein
    • Protein or peptide: Capsid protein
    • Protein or peptide: Putative neck protein
    • Protein or peptide: Major tail sheath 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-#8
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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #4: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 4 / Details: Tail tube protein / 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 #5: Baseplate hub assembly protein

MacromoleculeName: Baseplate hub assembly protein / type: protein_or_peptide / ID: 5 / Details: Tail terminator protein / 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 #6: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 6 / Details: Stopper protein / 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 #7: Putative neck protein

MacromoleculeName: Putative neck protein / type: protein_or_peptide / ID: 7 / Details: Adaptor protein / 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: Major tail sheath protein

MacromoleculeName: Major tail sheath protein / type: protein_or_peptide / ID: 8 / Details: Tail sheath protein / Number of copies: 3 / 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 #2: Anchor DNA forward strand (120-MER)

MacromoleculeName: Anchor DNA forward strand (120-MER) / type: dna / ID: 2 / Details: Random sequence / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 36.24227 KDa
SequenceString: (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT)(DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT)(DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT) (DC)(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT) (DC) (DT)(DA)(DC)(DA)(DC)(DT) ...String:
(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT)(DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT)(DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT) (DC)(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA)(DT) (DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA) (DT)(DC)(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DA) (DT)(DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT) (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DT)(DT) (DA)(DT)(DC) (DT)(DA)(DC)(DA)(DC)(DT) (DT)(DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DT) (DT)(DA)(DT)(DC) (DT)(DA)(DC)(DA)(DC) (DT)(DT)(DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC) (DT)(DT)(DA)(DT)(DC)

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Macromolecule #3: Anchor DNA reverse strand (120-MER)

MacromoleculeName: Anchor DNA reverse strand (120-MER) / type: dna / ID: 3 / Details: Random sequence / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
Molecular weightTheoretical: 37.79132 KDa
SequenceString: (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT)(DA) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT)(DA) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT) (DA)(DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT) (DA) (DG)(DA)(DT)(DA)(DA)(DG) ...String:
(DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT)(DA) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT)(DA) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT) (DA)(DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DT) (DA) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG) (DT)(DA)(DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG) (DT)(DA) (DG)(DA)(DT)(DA)(DA)(DG)(DT) (DG)(DT)(DA)(DG)(DA)(DT)(DA)(DA)(DG)(DT) (DG)(DT)(DA) (DG)(DA)(DT)(DA)(DA)(DG) (DT)(DG)(DT)(DA)(DG)(DA)(DT)(DA)(DA)(DG) (DT)(DG)(DT)(DA) (DG)(DA)(DT)(DA)(DA) (DG)(DT)(DG)(DT)(DA)(DG)(DA)(DT)(DA)(DA) (DG)(DT)(DG)(DT)(DA)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 3 / 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

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER
Software:
Namedetails
RELION (ver. 3.1)
UCSF Chimera (ver. 1.16)vop maximum

Details: Composite map created by merging three reconstructions and low-pass filtered to the resolution of the worst-resolved input reconstruction. The resolutions of the input maps were determined ...Details: Composite map created by merging three reconstructions and low-pass filtered to the resolution of the worst-resolved input reconstruction. The resolutions of the input maps were determined by gold-standard FSC at 0.143.
Number images used: 17304
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)

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Atomic model buiding 1

Initial model
PDB IDChain

8q7d

source_name: PDB, initial_model_type: experimental model

8q01

source_name: PDB, initial_model_type: experimental model

8q1i

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qek:
Neck and tail of phage 812 after tail contraction (composite)

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