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- EMDB-55951: Phage 812 baseplate in the pre-contraction state (C3) -

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Basic information

Entry
Database: EMDB / ID: EMD-55951
TitlePhage 812 baseplate in the pre-contraction state (C3)
Map dataPhage 812 baseplate in the pre-contraction state (C3); postprocessed map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: x 15 types
Keywordsphage / baseplate / VIRUS
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / hydrolase activity, acting on glycosyl bonds / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process / proteolysis
Similarity search - Function
Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Putative phage tail tube initiator protein / : / Lid domain of Phi812 weld protein / : / Phi812 tail tube protein / : / ORF68-like, C-terminal domain ...Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Putative phage tail tube initiator protein / : / Lid domain of Phi812 weld protein / : / 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 / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / CHAP domain profile. / CHAP domain / CHAP domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / LysM domain superfamily / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
CBM-cenC domain-containing protein / ORF68 / ORF67 / ORF65 / ORF64 / ORF63 / ORF62 / ORF61 / ORF60 / ORF59 ...CBM-cenC domain-containing protein / ORF68 / ORF67 / ORF65 / ORF64 / ORF63 / ORF62 / ORF61 / ORF60 / ORF59 / ORF58 / ORF57 / ORF56 / ORF50 / ORF49
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 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: EMBO J / Year: 2026
Title: Conformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812.
Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos ...Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos Tripsianes / Pavel Plevka /
Abstract: Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of ...Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.
History
DepositionDec 5, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55951.png

Downloads & links

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Map

FileDownload / File: emd_55951.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the pre-contraction state (C3); postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 640 pix.
= 1067.008 Å		1.67 Å/pix.
x 640 pix.
= 1067.008 Å		1.67 Å/pix.
x 640 pix.
= 1067.008 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: 0.025
Minimum - Maximum-0.04604272 - 0.10633341
Average (Standard dev.)0.00032543344 (±0.0031405482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1067.0079 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55951_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 (C3); half map 1

Fileemd_55951_half_map_1.map
AnnotationPhage 812 baseplate in the pre-contraction state (C3); half map 1
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 (C3); half map 2

Fileemd_55951_half_map_2.map
AnnotationPhage 812 baseplate in the pre-contraction state (C3); half map 2
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: ORF68
    • Protein or peptide: ORF64
    • Protein or peptide: ORF65
    • Protein or peptide: ORF58
    • Protein or peptide: CBM-cenC domain-containing protein
    • Protein or peptide: ORF50
    • Protein or peptide: ORF49
    • Protein or peptide: ORF57
    • Protein or peptide: ORF56
    • Protein or peptide: ORF60
    • Protein or peptide: ORF59
    • Protein or peptide: ORF61
    • Protein or peptide: ORF62
    • Protein or peptide: ORF63
    • Protein or peptide: ORF67

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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: ORF68

MacromoleculeName: ORF68 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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 #2: ORF64

MacromoleculeName: ORF64 / type: protein_or_peptide / ID: 2 / Number of copies: 24 / 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: 12 / 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: ORF58

MacromoleculeName: ORF58 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 96.199547 KDa
SequenceString: MVVRFQSSMG RSLKRVDSDD LNVKGLVLAT VSKINYKYQS VEVKVNNLTL GSRIGDDGSL AVPYPKSFIG RTPEGSVFGT KPLITEGSV VLIGFLNDDI NSPIILSVYG DNEQNKMINT NPLDGGKFDT ESVYKYSSSL YEILPSLNYK YDDGEGTSIR T YNGKSFFS ...String:
MVVRFQSSMG RSLKRVDSDD LNVKGLVLAT VSKINYKYQS VEVKVNNLTL GSRIGDDGSL AVPYPKSFIG RTPEGSVFGT KPLITEGSV VLIGFLNDDI NSPIILSVYG DNEQNKMINT NPLDGGKFDT ESVYKYSSSL YEILPSLNYK YDDGEGTSIR T YNGKSFFS MTSGEEEKPQ ATDFYTGTEY QDLFTSYYGN KTLIEPRIQK APNMLFKHQG VFYDDGTPDN HITTLFISER GD IRASVLN TETQKRTTQE MSSDGSYRVI KQDDDLMLDE AQVWIEYGIS EDNKFYIKND KHKFEFTDEG IYIDDKPMLE NLD ESIAEA MKNLNEIQKE LDDINYLLKG VGKDNLEELI ESTKESIEAS KKATSDVNRL TTQIAEVSGR TEGIITQFQK FRDE TFKDF YEDASTVINE VNQNFPTMKT DVKTLKTKVD NLEKTEIPNI KTRLTELENN NNNADKIISD RGEHIGAMIQ LEENV TVPM RKYMPIPWSK VTYNNAEFWD SNNPTRLVVP KGITKVRVAG NVLWDSNATG QRMLRILKNG TYSIGLPYTR DVAIST APQ NGTSGVIPVK EGDYFEFEAF QDSEGDRQFR ADPYTWFSIE AIELETETME KDFMLIGHRG ATGYTDEHTI KGYQMAL DK GADYIELDLQ LTKDNKLLCM HDSTIDRTTT GTGKVGDMTL SYIQTNFTSL NGEPIPSLDD VLNHFGTKVK YYIETKRP F DANMDRELLT QLKAKGLIGI GSERFQVIIQ SFARESLINI HNQFSNIPLA YLTSTFSESE MDDCLSYGFY AIAPKYTTI TKELVDLAHS KGLKVHAWTV NTKEEMQSLI QMGVDGFFTN YLDEYKKI

UniProtKB: ORF58

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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: 6 / 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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Macromolecule #6: ORF50

MacromoleculeName: ORF50 / type: protein_or_peptide / ID: 6 / 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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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: ORF57

MacromoleculeName: ORF57 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 34.645887 KDa
SequenceString: MATDKEAKDV IDKFIDNVFN FDVLTKERIK EKDEEIKKIT TDDMYEKVVY IRPYVGVIQS LNPQHVQYES FSNNGYDIEA ELSFRKVSY LVDKGSIPTD SLSTLTVHLV ERNQELLIDY FDEIQDVLYG EYMEEEYVFD EDVPLSTILA LDLNDNLKSL S NIKYMFKG ...String:
MATDKEAKDV IDKFIDNVFN FDVLTKERIK EKDEEIKKIT TDDMYEKVVY IRPYVGVIQS LNPQHVQYES FSNNGYDIEA ELSFRKVSY LVDKGSIPTD SLSTLTVHLV ERNQELLIDY FDEIQDVLYG EYMEEEYVFD EDVPLSTILA LDLNDNLKSL S NIKYMFKG APKENPFGTD KDVYIDTYNL LYWLYLGEDE ELAYPMNINY FFTEGRFFTI FGKGHKYKVD VSKFIVGDIL FF GRSDTNI GIYVGDGEFI SMMGKFPKDE TPIGKYKLDD YWNEFNGRVM RFDEEVYI

UniProtKB: ORF57

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Macromolecule #9: ORF56

MacromoleculeName: ORF56 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 91.364289 KDa
SequenceString: MRRIRRPKVR IEIVTDDNTF TLRFEDTRDY NGDEFGAKLL GFQTKNSMED DSSVFQINMA GDTYWDKLVM ANDIIRIFIT PNDDPNDKE GKQERLIQVG MVSQVSKVGS YGNDQTQFRI TGQSFVKPFM KFGLGVIQEV QAVLPEVGWL IDGDGDNEVK F TGSSAHEV ...String:
MRRIRRPKVR IEIVTDDNTF TLRFEDTRDY NGDEFGAKLL GFQTKNSMED DSSVFQINMA GDTYWDKLVM ANDIIRIFIT PNDDPNDKE GKQERLIQVG MVSQVSKVGS YGNDQTQFRI TGQSFVKPFM KFGLGVIQEV QAVLPEVGWL IDGDGDNEVK F TGSSAHEV MTGIIRRFIP YMKYNYTEKT YNTIDNYLDY DDLSSWDEFE KLTEVSAFTN FDGSLKQLMD MVTARPFNEL FF KNSEKTP GKAQLVLRKT PFNPTEWRAL DMIKVPTEDF IEEDVGKSDV ETYSIFTATP AGMLKELNGD VFSKPQFHPE LTD RYGYTK FEVENIYLST KSGSATEDSD SSGDDNGTER GTYSKIMKDL SNYGRDNISK GIDKYTSKLS SKYKNLKKAQ AKKI IEKFV KEGKVTEKEY EKITGNKVDD ELTSDNRPKL TKDKLKSILK EKFKTQDDFN NSKKKKKAKT DALKELTTKY RFGNK THAT TLLDEYIKYK GEPPNDEAFD KYLKAIEGVS NVATDTGSDA SDSPLVMFSR MLFNWYHGNP NFYAGDIIVL GDPKYD LGK RLFIEDKQRG DTWEFYIESV EHKFDYKQGY YTTVGVTRGL KDAILEDGKG SPHRFAGLWN QSSDFMGGLM GEDTSKE LK EKGVAEKQSS GDKDGGSDSG GAQDGGSLDS LKKYNGKLPK HDPSFVQPGN RHYKYQCTWY AYNRRGQLGI PVPLWGDA A DWIGGAKGAG YGVGRTPKQG ACVIWQRGVQ GGSPQYGHVA FVEKVLDGGK KIFISEHNYA TPNGYGTRTI DMSSAIGKN AQFIYDKK

UniProtKB: ORF56

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Macromolecule #10: ORF60

MacromoleculeName: ORF60 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 19.998748 KDa
SequenceString:
MNNFIPQPQG LLRFLNTLDT DLTSSHMNLL DEEVSFVSKF YTPQLQLSEL AKKVLTNIKT DDIPVLEREF NDNTIIHKAN DTLLKVQAP RMYMILQSIV LEAYAIVNCF VENPSSLKYL TEEDVSITRE NLNYVADYLG NYDDYNSVVL DLRDLDLCFS A IELQLPLI KKEANV

UniProtKB: ORF60

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Macromolecule #11: ORF59

MacromoleculeName: ORF59 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 29.381604 KDa
SequenceString: MPQSDGISNL HRIALRFPKE GGGYDMYRFK VNPENYTIDS PQRTTAIKTK SDIVIEDYGK DIEVINFTGT TGFRPVREAD GLKTGKQKM EELQSRVSEY AMQGGSGNVS GSYLQFFNFT DDSYYKVHLA PQGLKITRSK DEPLLFRYEI TLVVIGSLTE A DRSAVTTE ...String:
MPQSDGISNL HRIALRFPKE GGGYDMYRFK VNPENYTIDS PQRTTAIKTK SDIVIEDYGK DIEVINFTGT TGFRPVREAD GLKTGKQKM EELQSRVSEY AMQGGSGNVS GSYLQFFNFT DDSYYKVHLA PQGLKITRSK DEPLLFRYEI TLVVIGSLTE A DRSAVTTE EFGNVKPNAS QRVDEGIKEL DKNARKTRDR NNQEISRREN TIPKSTGDNT NEGNRLKQSF PSSSIYNPRQ ST NGLKGNI DNMALIIGYG DGGVSS

UniProtKB: ORF59

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Macromolecule #12: ORF61

MacromoleculeName: ORF61 / type: protein_or_peptide / ID: 12 / 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 #13: ORF62

MacromoleculeName: ORF62 / type: protein_or_peptide / ID: 13 / Number of copies: 4 / 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 #14: ORF63

MacromoleculeName: ORF63 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / 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 #15: ORF67

MacromoleculeName: ORF67 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 14.627471 KDa
SequenceString:
MAVKYDIGNN EIVLHLREGK YITGFTTVGG YDKELGQVKV NREILPAYFF DNFAYERYLY YSKPEEVIEN KNYVPPQIND DDEESQQIT VPKEQYDSLK EELELMRKQQ EAMMEMLQKL LGQKG

UniProtKB: ORF67

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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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 3586
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. lower arm, upper arm, core, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (all chains as a single rigid body).
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 287
Output model

PDB-9tic:
Phage 812 baseplate in the pre-contraction state (C3)

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