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- EMDB-55953: Phage 812 baseplate in the pre-contraction state - tail sheath in... -

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Basic information

Entry
Database: EMDB / ID: EMD-55953
TitlePhage 812 baseplate in the pre-contraction state - tail sheath initiator and baseplate-proximal tail proteins
Map dataPhage 812 baseplate in the pre-contraction state - tail sheath initiator and proximal tail proteins; postprocessed map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: ORF61
    • Protein or peptide: ORF49
    • Protein or peptide: ORF50
Keywordsphage / baseplate / VIRUS
Function / homology: / Phi812 tail tube protein / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / LysM domain superfamily / LysM domain / ORF61 / ORF50 / ORF49
Function and homology information
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBinovsky J / Plevka P
Funding supportEuropean Union, Czech Republic, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Conformational changes of baseplate regulating tail contraction of Staphylococcus phage 812
Authors: Binovsky J / Plevka P
History
DepositionDec 5, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55953.png

Downloads & links

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Map

FileDownload / File: emd_55953.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the pre-contraction state - tail sheath initiator and proximal tail proteins; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.06419192 - 0.11005041
Average (Standard dev.)0.00017596949 (±0.0029859436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55953_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage 812 baseplate in the pre-contraction state -...

Fileemd_55953_half_map_1.map
AnnotationPhage 812 baseplate in the pre-contraction state - tail sheath initiator and proximal tail proteins; half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage 812 baseplate in the pre-contraction state -...

Fileemd_55953_half_map_2.map
AnnotationPhage 812 baseplate in the pre-contraction state - tail sheath initiator and proximal tail proteins; half map2
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 812K1/420

EntireName: Staphylococcus phage 812K1/420 (virus)
Components
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: ORF61
    • Protein or peptide: ORF49
    • Protein or peptide: ORF50

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Supramolecule #1: Staphylococcus phage 812K1/420

SupramoleculeName: Staphylococcus phage 812K1/420 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Propagated in S. aureus SA 812 (CCM 4028) planktonic culture and purified on a CsCl gradient.
NCBI-ID: 3434241 / Sci species name: Staphylococcus phage 812K1/420 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: ORF61

MacromoleculeName: ORF61 / type: protein_or_peptide / ID: 1 / Details: tail sheath initoator protein / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 26.611752 KDa
SequenceString: MRFKKHVVQH EETMQAIAQR YYGDVSYWID LVEHNNLKYP YLVETDEEKM KDPERLASTG DTLIIPIESD LTDVSAKEIN SRDKDVLVE LALGRDLNIT ADEKYFNEHG TSDNILAFST NGNGDLDTVK GIDNMKQQLQ ARLLTPRGSL MLHPNYGSDL H NLFGLNIP ...String:
MRFKKHVVQH EETMQAIAQR YYGDVSYWID LVEHNNLKYP YLVETDEEKM KDPERLASTG DTLIIPIESD LTDVSAKEIN SRDKDVLVE LALGRDLNIT ADEKYFNEHG TSDNILAFST NGNGDLDTVK GIDNMKQQLQ ARLLTPRGSL MLHPNYGSDL H NLFGLNIP EQATLIEMEV LRTLTSDNRV KSANLIDWKI QGNVYSGQFS VEIKSVEESI NFVLGQDEEG IFALFE

UniProtKB: ORF61

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Macromolecule #2: ORF49

MacromoleculeName: ORF49 / type: protein_or_peptide / ID: 2 / Details: tail sheath protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
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: ORF49

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Macromolecule #3: ORF50

MacromoleculeName: ORF50 / type: protein_or_peptide / ID: 3 / Details: tail tube protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 15.94297 KDa
SequenceString:
MASEAKQTVH TGNTVLLMIK GKPVGRAQSA SGQREYGTTG VYEIGSIMPQ EHVYLRYEGT ITVERLRMKK ENFADLGYAS LGEEILKKD IIDILVVDNL TKQVIISYHG CSANNYNETW QTNEIVTEEI EFSYLTASDK ART

UniProtKB: ORF50

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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 mMTristris
10.0 mMNaClsodium chloride
10.0 mMCaCl2calcium 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. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: Blot time 6, blot force -2.
Details10e9 PFU/ml

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 26731 / Average exposure time: 2.0 sec. / Average electron dose: 40.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 64874
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING ONLY
Startup modelType of model: EMDB MAP
EMDB ID:

8210

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 4071
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 40.72
Output model

PDB-9tie:
Phage 812 baseplate in the pre-contraction state - tail sheath initiator and baseplate-proximal tail proteins

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