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- EMDB-55969: Baseplate arm (segment B) of phage 812 in the post-contraction state -

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Basic information

Entry
Database: EMDB / ID: EMD-55969
TitleBaseplate arm (segment B) of phage 812 in the post-contraction state
Map dataBaseplate arm (segment B) of phage 812 in the post-contraction state; postprocessed map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: ORF64
    • Protein or peptide: ORF63
    • Protein or peptide: ORF65
Keywordsphage / baseplate / VIRUS
Function / homologyDomain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / ORF65 / ORF64 / ORF63
Function and homology information
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBinovsky J / Plevka P / Baska R / Pichel-Beleiro A / Skubnik K / Novacek J / van Raaij MJ
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_55969.png

Downloads & links

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Map

FileDownload / File: emd_55969.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBaseplate arm (segment B) of phage 812 in the post-contraction state; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.592 Å		1.06 Å/pix.
x 256 pix.
= 270.592 Å		1.06 Å/pix.
x 256 pix.
= 270.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.047925457 - 0.07543084
Average (Standard dev.)0.00011892607 (±0.001930451)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55969_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Baseplate arm (segment B) of phage 812 in...

Fileemd_55969_half_map_1.map
AnnotationBaseplate arm (segment B) of phage 812 in the post-contraction state; half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Baseplate arm (segment B) of phage 812 in...

Fileemd_55969_half_map_2.map
AnnotationBaseplate arm (segment B) of phage 812 in the post-contraction state; half map1
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: ORF64
    • Protein or peptide: ORF63
    • Protein or peptide: ORF65

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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: ORF64

MacromoleculeName: ORF64 / type: protein_or_peptide / ID: 1 / Details: arm segment protein / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 19.259613 KDa
SequenceString:
MAIATYNSHV ELAKYLVSKA DSVYLTIGKS TPWSNETNPP QPDENATVLQ EVIGYKKATK VTLVRPSKSP EDDNKNLISY GNKSWVEVT PENAKAEGAK WVYLESSIVG DELPLGTYRQ VGFVMDLVAK SGISKFNLVP SEVESTGTLL FFDNKQFQNR S EQTTAKER FIVEV

UniProtKB: ORF64

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Macromolecule #2: ORF63

MacromoleculeName: ORF63 / type: protein_or_peptide / ID: 2 / Details: arm scaffold protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 116.389945 KDa
SequenceString: MANFLKNLHP LLRRDRNKKD NQDPNFALID ALNEEMNQVE KDAIESKLQS SLKTSTSEYL DKFGDWFGVY RKTDEKDDVY RARIIKYLL LKRGTNNAII DAIKDYLGRD DIDVSVYEPF TNIFYTNKSH LNGEDHLMGY YYRFAVINVS IGDYFPVEII D VINEFKPA ...String:
MANFLKNLHP LLRRDRNKKD NQDPNFALID ALNEEMNQVE KDAIESKLQS SLKTSTSEYL DKFGDWFGVY RKTDEKDDVY RARIIKYLL LKRGTNNAII DAIKDYLGRD DIDVSVYEPF TNIFYTNKSH LNGEDHLMGY YYRFAVINVS IGDYFPVEII D VINEFKPA GVTLYVTYDG ASTIRGGAII KWLDGLPKIE TYQEFDRFTG YDDTFYGHIN MNQSKDTDNS SSDIFKTNHS LI NSLDVLT GSSSVGRQYI NYGYVTSYVY NPGMTSSVNQ ISASTEGRGQ EVPTDYYMYT STKNNNTVEL SMQTTSGVSY LYN NFNFRD YMSKYRPQVD LQSDEARRIV SDYIKELSID YYLSAVIPPD ESIEIKLQVY DFSINRWLTV SINNLSFYEK NIGS NIGYI KDYLNSELNM FTRLEINAGK RDSVDIKVNY LDLMFYYYER GIYTIKPYKA LIENYLDISR ETYVEAFKIA SLSNG DIIT KTGFQPIGYL KLVGNYENTI PSTINIVAKD TDNNPIESNE LDVYNTVENR NLLQSYKGVN TIAREITSTK EFTVSG WAK EIYSTNYLSK VLKPGKVYTL SFDMEITGND PTLKSYSDNH GIYLYSNTKG IVVNGVKSME RTIGNKVSVT QTFTAPT IT DHRLLIYTGR YTSDGKASTP PVFFNTVKIT ELKLTEGSSK LEYSPAPEDK PNVIEKGIKF NNILTNIQTL SINSDTIL K NVTLYYSYYG DSWVELKTLG NISTGETTET NNLIDLYGLQ TVDYSNINPM SKVSLRSIWN VKLGELNNQE GSLSNMPND YFNAVWQDID KLSDIELGSM RMVKDTEGGV FDGATGEIIK ATLFNVGAYT DLDMLAYTLT NYTEPLTLGS SRLISELKEE LLTSESFNV DNRIKVIDSI YEELPNTSII KNGFVEREVT GSKYLDYGLY EPIEDGTRYK LIVEGEFKDN IEFISLYNSN P NFNETFIY PSEIINGVAE KEFIAKPSTE DKPRLNTDVR IYIRPYDSTI SKVRRVELRK V

UniProtKB: ORF63

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Macromolecule #3: ORF65

MacromoleculeName: ORF65 / type: protein_or_peptide / ID: 3 / Details: tripod protein / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 129.262961 KDa
SequenceString: MAINFKGSPY LDRFDPSKDR TKVLFNPDRP LQQAELNEMQ SIDQYYLKNL GDAIFKDGDK QSGLGFTLSE DNVLTVNPGY VYINGKIRY YDNDDSVKIT GVGKETIGIK LTERIVTPDE DASLLDQTSG VPSYFSKGAD RLEEKMSLTV NDPTSATIYT F MDGDLYIQ ...String:
MAINFKGSPY LDRFDPSKDR TKVLFNPDRP LQQAELNEMQ SIDQYYLKNL GDAIFKDGDK QSGLGFTLSE DNVLTVNPGY VYINGKIRY YDNDDSVKIT GVGKETIGIK LTERIVTPDE DASLLDQTSG VPSYFSKGAD RLEEKMSLTV NDPTSATIYT F MDGDLYIQ STNAEMDKIN KVLAERTYDE SGSYKVNGFE LFSEGNAEDD DHVSVVVDAG KAYVKGFKVD KPVSTRISVP KS YDLGTAE NESTIFNKSN NSISLANSPV KEIRRVTGQV LIEKERVTRG AQGDGQDFLS NNTAFEIVKV WTETSPGVTT KEY KQGEDF RLTDGQTIDW SPQGQEPSGG TSYYVSYKYN KRMEAGKDYE VTTQGEGLSK KWYINFTPSN GAKPIDQTVV LVDY TYYLA RKDSVFINKY GDIAILPGEP NIMRLVTPPL NTDPENLQLG TVTVLPDSDE AVCISFAITR LSMEDLQKVK TRVDN LEYN QAVNALDDGA MEGQNPLTLR SVFSEGFISL DKADITHPDF GIVFSFEDAE ATLAYTEAVN QPKIIPGDTT AHIWGR LIS APFTEERTIY QGQASETLNV NPYNIPNKQG VLKLTPSEDN WIDTENVTIT EQKTKKVTMK RFWRHNESYY GETEHYL YS NLQLDAGQKW KGETYAYDRE HGRTGTLLES GGQRTLEEMI EFIRIRDVSF EVKGLNPNDN NLYLLFDGVR CAITPATG Y RKGSEDGTIM TDAKGTAKGK FTIPAGIRCG NREVTLKNAN STSATTYTAQ GRKKTAQDII IRTRVTVNLV DPLAQSFQY DENRTISSLG LYFASKGDKQ SNVVIQIRGM GDQGYPNKTI YAETVMNADD IKVSNNASAE TRVYFDDPMM AEGGKEYAIV IITENSDYT MWVGTRTKPK IDKPNEVISG NPYLQGVLFS SSNASTWTPH QNSDLKFGIY TSKFNETATI EFEPIKDVSA D RIVLMSTY LTPERTGCTW EMKLILDDMA SSTTFDQLKW EPIGNYQDLD VLGLARQVKL RATFESNRYI SPLMSSSDLT FT TFLTELT GSYVGRAIDM TEAPYNTVRF SYEAFLPKGT KVVPKYSADD GKTWKTFTKS PTTTRANNEF TRYVIDEKVK SSG TNTKLQ VRLDLSTENS FLRPRVRRLM VTTRDE

UniProtKB: ORF65

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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 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / 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: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 54841
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

8212

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 56778
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9tit:
Baseplate arm (segment B) of phage 812 in the post-contraction state

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