[English] 日本語
Yorodumi
- EMDB-19969: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19969
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, wedge module, and proximal tail proteins
Map dataPhage phi812 baseplate in the pre-contraction state - core, wedge modules, proximal tail; postprocessed map
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Complex: Tail
      • Complex: Tail tube
        • Protein or peptide: Capsid protein
      • Complex: Tail sheath
        • Protein or peptide: Major tail sheath protein
      • Complex: Baseplate
        • Protein or peptide: Peptidase C51 domain-containing protein
        • Protein or peptide: TmpF
        • Protein or peptide: Baseplate wedge subunit
        • Protein or peptide: Baseplate component
        • Protein or peptide: Putative baseplate component
        • Protein or peptide: Baseplate component
        • Protein or peptide: GP-PDE domain-containing protein
        • Protein or peptide: NlpC/P60 domain-containing protein
Keywordsbacteriophage / phage / contractile / phi812 / baseplate / VIRUS
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process
Similarity search - Function
Putative phage tail tube initiator protein / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / CHAP domain profile. / CHAP domain / CHAP domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Baseplate protein J-like ...Putative phage tail tube initiator protein / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / CHAP domain profile. / CHAP domain / CHAP domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Baseplate protein J-like / Baseplate J-like protein / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / LysM domain superfamily / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Baseplate component / Baseplate wedge subunit / NlpC/P60 domain-containing protein / Baseplate component / GP-PDE domain-containing protein / TmpF / Major tail sheath protein / Peptidase C51 domain-containing protein / Putative baseplate component / Capsid protein
Similarity search - Component
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBinovsky J / Siborova M / Baska R / Pichel-Beleiro A / Skubnik K / Novacek J / van Raaij MJ / 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: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky J / Siborova M / Baska R / Pichel-Beleiro A / Skubnik K / Novacek J / van Raaij MJ / Plevka P
History
DepositionMar 27, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19969.png

Downloads & links

-
Map

FileDownload / File: emd_19969.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage phi812 baseplate in the pre-contraction state - core, wedge modules, proximal tail; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 840 pix.
= 903. Å		1.08 Å/pix.
x 840 pix.
= 903. Å		1.08 Å/pix.
x 840 pix.
= 903. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.075 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07574776 - 0.109944545
Average (Standard dev.)0.00005555813 (±0.002117132)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions840840840
Spacing840840840
CellA=B=C: 903.00006 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19969_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Phage phi812 baseplate in the pre-contraction state -...

Fileemd_19969_half_map_1.map
AnnotationPhage phi812 baseplate in the pre-contraction state - core, wedge modules, proximal tail; half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Phage phi812 baseplate in the pre-contraction state -...

Fileemd_19969_half_map_2.map
AnnotationPhage phi812 baseplate in the pre-contraction state - core, wedge modules, proximal tail; half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Staphylococcus phage 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)
    • Complex: Tail
      • Complex: Tail tube
        • Protein or peptide: Capsid protein
      • Complex: Tail sheath
        • Protein or peptide: Major tail sheath protein
      • Complex: Baseplate
        • Protein or peptide: Peptidase C51 domain-containing protein
        • Protein or peptide: TmpF
        • Protein or peptide: Baseplate wedge subunit
        • Protein or peptide: Baseplate component
        • Protein or peptide: Putative baseplate component
        • Protein or peptide: Baseplate component
        • Protein or peptide: GP-PDE domain-containing protein
        • Protein or peptide: NlpC/P60 domain-containing protein

+
Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #4, #6-#7, #5, #8, #3, #2, #1, #10, #9 / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

+
Supramolecule #2: Tail

SupramoleculeName: Tail / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4, #6-#7, #5, #8, #3, #2, #1, #10, #9
Source (natural)Organism: Staphylococcus phage 812 (virus)

+
Supramolecule #3: Tail tube

SupramoleculeName: Tail tube / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #10
Source (natural)Organism: Staphylococcus phage 812 (virus)

+
Supramolecule #4: Tail sheath

SupramoleculeName: Tail sheath / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #9
Source (natural)Organism: Staphylococcus phage 812 (virus)

+
Supramolecule #5: Baseplate

SupramoleculeName: Baseplate / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #4, #6-#7, #5, #8, #3, #2, #1
Source (natural)Organism: Staphylococcus phage 812 (virus)

+
Macromolecule #1: NlpC/P60 domain-containing protein

MacromoleculeName: NlpC/P60 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: NlpC/P60 domain-containing protein

+
Macromolecule #2: GP-PDE domain-containing protein

MacromoleculeName: GP-PDE domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: GP-PDE domain-containing protein

+
Macromolecule #3: Baseplate component

MacromoleculeName: Baseplate component / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: Baseplate component

+
Macromolecule #4: Peptidase C51 domain-containing protein

MacromoleculeName: Peptidase C51 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: Peptidase C51 domain-containing protein

+
Macromolecule #5: Baseplate component

MacromoleculeName: Baseplate component / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: Baseplate component

+
Macromolecule #6: TmpF

MacromoleculeName: TmpF / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: TmpF

+
Macromolecule #7: Baseplate wedge subunit

MacromoleculeName: Baseplate wedge subunit / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: Baseplate wedge subunit

+
Macromolecule #8: Putative baseplate component

MacromoleculeName: Putative baseplate component / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: Putative baseplate component

+
Macromolecule #9: Major tail sheath protein

MacromoleculeName: Major tail sheath protein / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (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: Major tail sheath protein

+
Macromolecule #10: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 10 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 15.94297 KDa
SequenceString:
MASEAKQTVH TGNTVLLMIK GKPVGRAQSA SGQREYGTTG VYEIGSIMPQ EHVYLRYEGT ITVERLRMKK ENFADLGYAS LGEEILKKD IIDILVVDNL TKQVIISYHG CSANNYNETW QTNEIVTEEI EFSYLTASDK ART

UniProtKB: Capsid protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 48.0 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: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 23421
Startup modelType of model: EMDB MAP
EMDB ID:

8210

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 9705
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: C3 symmetry imposed
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9eug:
Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, wedge module, and proximal tail proteins

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more