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- EMDB-55978: Phage 812 baseplate in the post-contraction state - composite -

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Basic information

Entry
Database: EMDB / ID: EMD-55978
TitlePhage 812 baseplate in the post-contraction state - composite
Map dataPhage 812 baseplate in the post-contraction state - composite
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: ORF61
    • Protein or peptide: ORF62
    • Protein or peptide: ORF63
    • Protein or peptide: ORF64
    • Protein or peptide: ORF65
    • Protein or peptide: ORF68
    • Protein or peptide: ORF49
  • Protein or peptide: ORF50
Keywordsphage / baseplate / VIRUS
Function / homology
Function and homology information


: / Phi812 tail tube protein / : / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / Protein of unknown function DUF2634 / Contractile injection system sheath initiator ...: / Phi812 tail tube protein / : / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Baseplate protein J-like / Baseplate J-like protein barrel domain / LysM domain superfamily / LysM domain
Similarity search - Domain/homology
ORF68 / ORF65 / ORF64 / ORF63 / ORF62 / ORF61 / ORF50 / ORF49
Similarity search - Component
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_55978.png

Downloads & links

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Map

FileDownload / File: emd_55978.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the post-contraction state - composite
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 680 pix.
= 718.76 Å		1.06 Å/pix.
x 680 pix.
= 718.76 Å		1.06 Å/pix.
x 680 pix.
= 718.76 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: 1.0
Minimum - Maximum0.0 - 4.0215373
Average (Standard dev.)0.048481934 (±0.17702873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 718.76 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 812K1/420

EntireName: Staphylococcus phage 812K1/420 (virus)
Components
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: ORF61
    • Protein or peptide: ORF62
    • Protein or peptide: ORF63
    • Protein or peptide: ORF64
    • Protein or peptide: ORF65
    • Protein or peptide: ORF68
    • 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: #1-#7
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 / Number of copies: 1 / 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: ORF62

MacromoleculeName: ORF62 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 39.248859 KDa
SequenceString: MKTRKLTNIL SKLIDKTMAG TSKITDFTPG SASRSLLEAV SLEIEQFYIL TKENIDWGIQ EGIIEAFDFQ KRQSKRAYGD VTIQFYQPL DMRMYIPAGT TFTSTRQEYP QQFETLVDYY AEPDSTEIVV EVYCKETGVA GNVPEGTINT IASGSSLIRS V NNEYSFNT ...String:
MKTRKLTNIL SKLIDKTMAG TSKITDFTPG SASRSLLEAV SLEIEQFYIL TKENIDWGIQ EGIIEAFDFQ KRQSKRAYGD VTIQFYQPL DMRMYIPAGT TFTSTRQEYP QQFETLVDYY AEPDSTEIVV EVYCKETGVA GNVPEGTINT IASGSSLIRS V NNEYSFNT GTKEESQEDF KRRFHSFVES RGRATNKSVR YGALQIPDVE GVYVYEETGH ITVFAHDRNG NLSDTLKEDI ID ALQDYRP SGIMLDVTGV EKEEVNVSAT VTISNKSRIG DTLQKHIESV IRSYLNNLKT SDDLIITDLI QAIMNIDDVL IYD VSFDNL DENIIVPPQG IIRAGEIKVE LK

UniProtKB: ORF62

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Macromolecule #3: ORF63

MacromoleculeName: ORF63 / type: protein_or_peptide / ID: 3 / 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 #4: ORF64

MacromoleculeName: ORF64 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / 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 #5: ORF65

MacromoleculeName: ORF65 / type: protein_or_peptide / ID: 5 / 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 #6: ORF68

MacromoleculeName: ORF68 / type: protein_or_peptide / ID: 6 / 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 #7: ORF49

MacromoleculeName: ORF49 / type: protein_or_peptide / ID: 7 / 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 #8: ORF50

MacromoleculeName: ORF50 / type: protein_or_peptide / ID: 8 / Number of copies: 15 / 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 / 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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX
Details: As this is a composite map, the reported resolution is based on the constituent map with the lowest average resolution.
Number images used: 25483
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

DetailsFitting of previously refined sub-models (e.g. arm, core and wedge modules, baseplate-proximal tail sheath, tail tube) in ChimeraX as rigid bodies before the rigid body refinement in Phenix (all chains as a single rigid body).
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9tiw:
Phage 812 baseplate in the post-contraction state - composite

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