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- EMDB-48174: Clostridioides difficile Transferase B Component Trimer in Comple... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Clostridioides difficile Transferase B Component Trimer in Complex with the A Component | |||||||||
![]() | CDTb trimer-CDTa map. | |||||||||
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![]() | Toxin / Clostridioides / Iota / ADP-ribosyltransferase | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.86 Å | |||||||||
![]() | Sheedlo MJ / Mullard RM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Oligomerization of the Clostridioides difficile Transferase B Component Proceeds through a Stepwise Mechanism In Vitro Authors: Sheedlo MJ / Mullard RM | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 73.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.3 KB | Display | ![]() |
Images | ![]() | 28.1 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 139 MB 139 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 843.7 KB | Display | ![]() |
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Full document | ![]() | 843.3 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9mdnMC ![]() 9mdiC ![]() 9mdjC ![]() 9mdlC ![]() 9mdpC ![]() 9mdrC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | CDTb trimer-CDTa map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: CDTb trimer-CDTa half map B.
File | emd_48174_half_map_1.map | ||||||||||||
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Annotation | CDTb trimer-CDTa half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CDTb trimer-CDTa half map A.
File | emd_48174_half_map_2.map | ||||||||||||
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Annotation | CDTb trimer-CDTa half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Clostridioides difficile Transferase Component B dimer in complex...
Entire | Name: Clostridioides difficile Transferase Component B dimer in complex with the A Component |
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Components |
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-Supramolecule #1: Clostridioides difficile Transferase Component B dimer in complex...
Supramolecule | Name: Clostridioides difficile Transferase Component B dimer in complex with the A Component type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 274 KDa |
-Macromolecule #1: Adp-ribosyltransferase binding component
Macromolecule | Name: Adp-ribosyltransferase binding component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 98.916828 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKIQMRNKKV LSFLTLTAIV SQALVYPVYA QTSTSNHSNK KKEIVNEDIL PNNGLMGYYF TDEHFKDLKL MAPIKDGNLK FEEKKVDKL LDKDKSDVKS IRWTGRIIPS KDGEYTLSTD RDDVLMQVNT ESTISNTLKV NMKKGKEYKV RIELQDKNLG S IDNLSSPN ...String: MKIQMRNKKV LSFLTLTAIV SQALVYPVYA QTSTSNHSNK KKEIVNEDIL PNNGLMGYYF TDEHFKDLKL MAPIKDGNLK FEEKKVDKL LDKDKSDVKS IRWTGRIIPS KDGEYTLSTD RDDVLMQVNT ESTISNTLKV NMKKGKEYKV RIELQDKNLG S IDNLSSPN LYWELDGMKK IIPEENLFLR DYSNIEKDDP FIPNNNFFDP KLMSDWEDED LDTDNDNIPD SYERNGYTIK DL IAVKWED SFAEQGYKKY VSNYLESNTA GDPYTDYEKA SGSFDKAIKT EARDPLVAAY PIVGVGMEKL IISTNEHAST DQG KTVSRA TTNSKTESNT AGVSVNVGYQ NGFTANVTTN YSHTTDNSTA VQDSNGESWN TGLSINKGES AYINANVRYY NTGT APMYK VTPTTNLVLD GDTLSTIKAQ ENQIGNNLSP GDTYPKKGLS PLALNTMDQF SSRLIPINYD QLKKLDAGKQ IKLET TQVS GNFGTKNSSG QIVTEGNSWS DYISQIDSIS ASIILDTENE SYERRVTAKN LQDPEDKTPE LTIGEAIEKA FGATKK DGL LYFNDIPIDE SCVELIFDDN TANKIKDSLK TLSDKKIYNV KLERGMNILI KTPTYFTNFD DYNNYPSTWS NVNTTNQ DG LQGSANKLNG ETKIKIPMSE LKPYKRYVFS GYSKDPLTSN SIIVKIKAKE EKTDYLVPEQ GYTKFSYEFE TTEKDSSN I EITLIGSGTT YLDNLSITEL NSTPEILDEP EVKIPTDQEI MDAHKIYFAD LNFNPSTGNT YINGMYFAPT QTNKEALDY IQKYRVEATL QYSGFKDIGT KDKEMRNYLG DPNQPKTNYV NLRSYFTGGE NIMTYKKLRI YAITPDDREL LVLSVD UniProtKB: Adp-ribosyltransferase binding component |
-Macromolecule #2: Cdta (Adp-ribosyltransferase enzymatic component)
Macromolecule | Name: Cdta (Adp-ribosyltransferase enzymatic component) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.816914 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: YSEKVCNTTY KAPIERPEDF LKDKEKAKEW ERKEAERIEQ KLERSEKEAL ESYKKDSVEI SKYSQTRNYF YDYQIEANSR EKEYKELRN AISKNKIDKP MYVYYFESPE KFAFNKVIRT ENQNEISLEK FNEFKETIQN KLFKQDGFKD ISLYEPGKGD E KPTPLLMH ...String: YSEKVCNTTY KAPIERPEDF LKDKEKAKEW ERKEAERIEQ KLERSEKEAL ESYKKDSVEI SKYSQTRNYF YDYQIEANSR EKEYKELRN AISKNKIDKP MYVYYFESPE KFAFNKVIRT ENQNEISLEK FNEFKETIQN KLFKQDGFKD ISLYEPGKGD E KPTPLLMH LKLPRNTGML PYTNTNNVST LIEQGYSIKI DKIVRIVIDG KHYIKAEASV VSSLDFKDDV SKGDSWGKAN YN DWSNKLT PNELADVNDY MRGGYTAINN YLISNGPVNN PNPELDSKIT NIENALKREP IPTNLTVYRR SGPQEFGLTL TSP EYDFNK LENIDAFKSK WEGQALSYPN FISTSIGSVN MSAFAKRKIV LRITIPKGSP GAYLSAIPGY AGEYEVLLNH GSKF KINKI DSYKDGTITK LIVDATLIP UniProtKB: Cdta (Adp-ribosyltransferase enzymatic component) |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 9 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-9mdn: |