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- EMDB-55961: Phage 812 baseplate in the pre-contraction state - upper arm -

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Basic information

Entry
Database: EMDB / ID: EMD-55961
TitlePhage 812 baseplate in the pre-contraction state - upper arm
Map dataPhage 812 baseplate in the pre-contraction state - upper arm; postprocessed map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: ORF63
    • Protein or peptide: ORF64
    • Protein or peptide: ORF65
    • Protein or peptide: ORF68
    • Protein or peptide: CBM-cenC domain-containing protein
Keywordsphage / baseplate / VIRUS
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds
Similarity search - Function
: / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / Carbohydrate-binding, CenC-like / Carbohydrate binding domain
Similarity search - Domain/homology
CBM-cenC domain-containing protein / ORF68 / ORF65 / ORF64 / ORF63
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 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_55961.png

Downloads & links

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Map

FileDownload / File: emd_55961.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the pre-contraction state - upper arm; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 360 pix.
= 600.192 Å		1.67 Å/pix.
x 360 pix.
= 600.192 Å		1.67 Å/pix.
x 360 pix.
= 600.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6672 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.073954016 - 0.11194687
Average (Standard dev.)0.0003003968 (±0.0034657444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 600.192 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55961_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_55961_half_map_1.map
AnnotationPhage 812 baseplate in the pre-contraction state - upper arm; 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_55961_half_map_2.map
AnnotationPhage 812 baseplate in the pre-contraction state - upper arm; 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: ORF63
    • Protein or peptide: ORF64
    • Protein or peptide: ORF65
    • Protein or peptide: ORF68
    • Protein or peptide: CBM-cenC domain-containing protein

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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: ORF63

MacromoleculeName: ORF63 / type: protein_or_peptide / ID: 1 / 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 #2: ORF64

MacromoleculeName: ORF64 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / 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 #3: ORF65

MacromoleculeName: ORF65 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / 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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Macromolecule #4: ORF68

MacromoleculeName: ORF68 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 50.474078 KDa
SequenceString: MALNFTTITE NNVIRDLTTQ VNNIGEELTK ERNIFDITDD LVYNFNKSQK IKLTDDKGLT KSYGNITALR DIKEPGYYYI GARTLATLL DRPDMESLDV VLHVVPLDTS SKVVQHLYTL STNNNQIKML YRFVSGNSSS EWQFIQGLPS NKNAVISGTN I LDIASPGV ...String:
MALNFTTITE NNVIRDLTTQ VNNIGEELTK ERNIFDITDD LVYNFNKSQK IKLTDDKGLT KSYGNITALR DIKEPGYYYI GARTLATLL DRPDMESLDV VLHVVPLDTS SKVVQHLYTL STNNNQIKML YRFVSGNSSS EWQFIQGLPS NKNAVISGTN I LDIASPGV YFVMGMTGGM PSGVSSGFLD LSVDANDNRL ARLTDAETGK EYTSIKKPTG TYTAWKKEFE PKDMEKYLLS SI RDDGSAS FPLLVYTSDS KTFQQAIIDH IDRTGQTTFT FYVQGGVSGS PMSNSCRGLF MSDTPNTSSL HGVYNAIGTD GRN VTGSVV GSNWTSPKTS PSHKELWTGA QSFLSTGTTK NLSDDISNYS YVEVYTTHKT TEKTKGNDNT GTICHKFYLD GSGT YVCSG TFVSGDRTDT KPPITEFYRV GVSFKGSTWT LVDSAVQNSK TQYVTRIIGI NMP

UniProtKB: ORF68

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Macromolecule #5: CBM-cenC domain-containing protein

MacromoleculeName: CBM-cenC domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 72.654742 KDa
SequenceString: MAFNYTPLTE TQKLKDMYPK VNDIGNFLKT EVNLSDVKQI SQPDFNNILA SIPDSGNYYV TNSKGAPSGE ATAGFVRLDK RNVNYYKIY YSPYSSNKMY IKTYANGTVY DWISFKLDEG SLYNEGNTLN VKELTESTTQ YATLVNPPKE NLNTGWVNYK E SKNGVSSL ...String:
MAFNYTPLTE TQKLKDMYPK VNDIGNFLKT EVNLSDVKQI SQPDFNNILA SIPDSGNYYV TNSKGAPSGE ATAGFVRLDK RNVNYYKIY YSPYSSNKMY IKTYANGTVY DWISFKLDEG SLYNEGNTLN VKELTESTTQ YATLVNPPKE NLNTGWVNYK E SKNGVSSL VEFNPVNSTS TFKMIRKLPV QEQKPNLLKD SLFVYPETSY SNIKTDNWDT PPFWGYSSNS GRSGVRFRGE NT VQIDDGS DTYPSVVSNR FKMGKELSVG DTVTVSVYAK INDPALLKDN LVYFELAGYD TVDDTSKNPY TGGRREITAS EIT TEWKKY SFTFTIPENT IGASGVKVNY VSLLLRMNCS SSKGNGAVVY YALPKLEKSS KVTPFITHEN DVRKYDEIWS NWQE VISKD ELKGHSPVDI EYNDYFKYQW WKSEVNEKSL KDLAMTVPQG YHTFYCQGSI AGTPKGRSIR GTIQVDYDKC DPYRA NKFV KLLFTDTEGI PYTLYYGGYN QGWKPLKQSE TSTLLWKGTL DFGSTEAVNL NDSLDNYDLI EVTYWTRSAG HFSTKR LDI KNTSNLLYIR DFNISNDSTG SSVDFFEGYC TFPTRTSVQP GMVKSITLDG STNTTKVASW NEKERIKVYN IMGINRG

UniProtKB: CBM-cenC 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 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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 19727
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

DetailsFitting of previously refined sub-models (e.g. segment A, segment B, segment CDEF from the upper arm) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (rigid bodies selected: res. 95-472 of arm scaffold protein and dimers of arm segments A, B and C, dimer of arm segment D, dimer of arm segment E, dimer of arm segment F, trimer of tripod proteins, trimer of RBP1, trimer of RBP2, res. 489-752 of arm scaffold protein).
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 132.6
Output model

PDB-9tim:
Phage 812 baseplate in the pre-contraction state - upper arm

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