[English] 日本語
Yorodumi
- EMDB-55954: Phage 812 baseplate in the pre-contraction state - lower arm -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55954
TitlePhage 812 baseplate in the pre-contraction state - lower arm
Map dataPhage 812 baseplate in the pre-contraction state - lower arm; postprocessed map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: CBM-cenC domain-containing protein
    • Protein or peptide: ORF64
    • Protein or peptide: ORF57
    • Protein or peptide: ORF67
    • Protein or peptide: ORF65
    • Protein or peptide: ORF56
    • Protein or peptide: ORF68
    • Protein or peptide: ORF63
Keywordsphage / baseplate / VIRUS
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / hydrolase activity, acting on glycosyl bonds / cysteine-type peptidase activity / proteolysis
Similarity search - Function
Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Lid domain of Phi812 weld 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 DUF2977 / Protein of unknown function (DUF2977) / : / Lid domain of Phi812 weld protein / : / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / CHAP domain profile. / CHAP domain / CHAP domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
CBM-cenC domain-containing protein / ORF68 / ORF67 / ORF65 / ORF64 / ORF63 / ORF57 / ORF56
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 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

-
Structure visualization

Supplemental images

emd_55954.png

Downloads & links

-
Map

FileDownload / File: emd_55954.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the pre-contraction state - lower 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-0.05094027 - 0.097008444
Average (Standard dev.)0.00029076327 (±0.0032144112)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_55954_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Phage 812 baseplate in the pre-contraction state -...

Fileemd_55954_half_map_1.map
AnnotationPhage 812 baseplate in the pre-contraction state - lower arm; half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Phage 812 baseplate in the pre-contraction state -...

Fileemd_55954_half_map_2.map
AnnotationPhage 812 baseplate in the pre-contraction state - lower arm; half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Staphylococcus phage 812K1/420

EntireName: Staphylococcus phage 812K1/420 (virus)
Components
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Protein or peptide: CBM-cenC domain-containing protein
    • Protein or peptide: ORF64
    • Protein or peptide: ORF57
    • Protein or peptide: ORF67
    • Protein or peptide: ORF65
    • Protein or peptide: ORF56
    • Protein or peptide: ORF68
    • Protein or peptide: ORF63

-
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

-
Macromolecule #1: CBM-cenC domain-containing protein

MacromoleculeName: CBM-cenC domain-containing protein / type: protein_or_peptide / ID: 1 / 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

-
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

-
Macromolecule #3: ORF57

MacromoleculeName: ORF57 / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #4: ORF67

MacromoleculeName: ORF67 / type: protein_or_peptide / ID: 4 / 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

-
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

-
Macromolecule #6: ORF56

MacromoleculeName: ORF56 / type: protein_or_peptide / ID: 6 / 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

-
Macromolecule #7: ORF68

MacromoleculeName: ORF68 / type: protein_or_peptide / ID: 7 / 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

-
Macromolecule #8: ORF63

MacromoleculeName: ORF63 / type: protein_or_peptide / ID: 8 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details10e9 PFU/ml

-
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

+
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: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 22031
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsFitting of previously refined sub-models (e.g. segment A, segment B, segment C, segment DEF, uRBP1-lRBP2, lRBP1-uRBP2 from the lower arm) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (rigid bodies selected: lid domain of the weld protein, cleaver domains of the hub protein, 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: 191.1
Output model

PDB-9tif:
Phage 812 baseplate in the pre-contraction state - lower arm

+
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