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Yorodumi- EMDB-38547: Cryo-EM structure of the protomers of the C ring in the CW state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38547 | ||||||||||||
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Title | Cryo-EM structure of the protomers of the C ring in the CW state | ||||||||||||
Map data | Experimental map | ||||||||||||
Sample |
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Keywords | Flagellum / Flagellar motor / C ring / CheY / MOTOR PROTEIN | ||||||||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / phosphorelay signal transduction system / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / metal ion binding ...archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / phosphorelay signal transduction system / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||
Authors | Tan JX / Zhang L / Zhou Y / Zhu YQ | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the protomers of the C ring in the CW state Authors: Tan JX / Zhang L / Zhou Y / Zhu YQ | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38547.map.gz | 777.3 MB | EMDB map data format | |
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Header (meta data) | emd-38547-v30.xml emd-38547.xml | 26.5 KB 26.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38547_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_38547.png | 110.9 KB | ||
Filedesc metadata | emd-38547.cif.gz | 7.5 KB | ||
Others | emd_38547_additional_1.map.gz emd_38547_half_map_1.map.gz emd_38547_half_map_2.map.gz | 713.6 MB 765.1 MB 765.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38547 | HTTPS FTP |
-Validation report
Summary document | emd_38547_validation.pdf.gz | 1002.8 KB | Display | EMDB validaton report |
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Full document | emd_38547_full_validation.pdf.gz | 1002.4 KB | Display | |
Data in XML | emd_38547_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | emd_38547_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38547 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38547 | HTTPS FTP |
-Related structure data
Related structure data | 8xp1MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38547.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Experimental map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: DeepEMhancer sharpened map
File | emd_38547_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_38547_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_38547_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C ring-containing flagellar motor-hook complex in the CW state
Entire | Name: C ring-containing flagellar motor-hook complex in the CW state |
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Components |
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-Supramolecule #1: C ring-containing flagellar motor-hook complex in the CW state
Supramolecule | Name: C ring-containing flagellar motor-hook complex in the CW state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
-Supramolecule #2: Constitutively active mutant of CheY
Supramolecule | Name: Constitutively active mutant of CheY / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5 |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
-Supramolecule #3: C ring-containing flagellar motor-hook
Supramolecule | Name: C ring-containing flagellar motor-hook / type: cell / ID: 3 / Parent: 1 / Macromolecule list: #1-#4 |
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-Macromolecule #1: Flagellar motor switch protein FliN
Macromolecule | Name: Flagellar motor switch protein FliN / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 14.801823 KDa |
Sequence | String: MSDMNNPSDE NTGALDDLWA DALNEQKATT TKSAADAVFQ QLGGGDVSGA MQDIDLIMDI PVKLTVELGR TRMTIKELLR LTQGSVVAL DGLAGEPLDI LINGYLIAQG EVVVVADKYG VRITDIITPS ERMRRLSR UniProtKB: Flagellar motor switch protein FliN |
-Macromolecule #2: Flagellar M-ring protein
Macromolecule | Name: Flagellar M-ring protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 61.295645 KDa |
Sequence | String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE ...String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE QKSPSASVTV TLEPGRALDE GQISAVVHLV SSAVAGLPPG NVTLVDQSGH LLTQSNTSGR DLNDAQLKFA ND VESRIQR RIEAILSPIV GNGNVHAQVT AQLDFANKEQ TEEHYSPNGD ASKATLRSRQ LNISEQVGAG YPGGVPGALS NQP APPNEA PIATPPTNQQ NAQNTPQTST STNSNSAGPR STQRNETSNY EVDRTIRHTK MNVGDIERLS VAVVVNYKTL ADGK PLPLT ADQMKQIEDL TREAMGFSDK RGDTLNVVNS PFSAVDNTGG ELPFWQQQSF IDQLLAAGRW LLVLVVAWIL WRKAV RPQL TRRVEEAKAA QEQAQVRQET EEAVEVRLSK DEQLQQRRAN QRLGAEVMSQ RIREMSDNDP RVVALVIRQW MSNDHE UniProtKB: Flagellar M-ring protein |
-Macromolecule #3: Flagellar motor switch protein FliM
Macromolecule | Name: Flagellar motor switch protein FliM / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 37.901066 KDa |
Sequence | String: MGDSILSQAE IDALLNGDSD TKDEPTPGIA SDSDIRPYDP NTQRRVVRER LQALEIINER FARQFRMGLF NLLRRSPDIT VGAIRIQPY HEFARNLPVP TNLNLIHLKP LRGTGLVVFS PSLVFIAVDN LFGGDGRFPT KVEGREFTHT EQRVINRMLK L ALEGYSDA ...String: MGDSILSQAE IDALLNGDSD TKDEPTPGIA SDSDIRPYDP NTQRRVVRER LQALEIINER FARQFRMGLF NLLRRSPDIT VGAIRIQPY HEFARNLPVP TNLNLIHLKP LRGTGLVVFS PSLVFIAVDN LFGGDGRFPT KVEGREFTHT EQRVINRMLK L ALEGYSDA WKAINPLEVE YVRSEMQVKF TNITTSPNDI VVNTPFHVEI GNLTGEFNIC LPFSMIEPLR ELLVNPPLEN SR HEDQNWR DNLVRQVQHS ELELVANFAD IPLRLSQILK LKPGDVLPIE KPDRIIAHVD GVPVLTSQYG TVNGQYALRV EHL INPILN SLNEEQPK UniProtKB: Flagellar motor switch protein FliM |
-Macromolecule #4: Flagellar motor switch protein FliG
Macromolecule | Name: Flagellar motor switch protein FliG / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 36.890957 KDa |
Sequence | String: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ ...String: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ PAALAELTEV LNGLLDGQNL KRSKMGGVRT AAEIINLMKT QQEEAVITAV REFDGELAQK IIDEMFLFEN LV DVDDRSI QRLLQEVDSE SLLIALKGAE PPLREKFLRN MSQRAADILR DDLANRGPVR LSQVENEQKA ILLIVRRLAE TGE MVIGSG EDTYV UniProtKB: Flagellar motor switch protein FliG |
-Macromolecule #5: Chemotaxis protein CheY
Macromolecule | Name: Chemotaxis protein CheY / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 14.177512 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MADKELKFLV VDKFSTMRRI VRNLLKELGF NNVEEAEDGV DALNKLQAGG FGFIISDWNM PNMDGLELLK TIRADSAMSA LPVLMVTAE AKKENIIAAA QAGASGWVVK PFTAATLEEK LNKIFEKLGM UniProtKB: Chemotaxis protein CheY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2. | |||||||||||||||
Details | This sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: OTHER | ||||||||
Output model | PDB-8xp1: |