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Yorodumi- EMDB-28207: Clostridioides difficile binary toxin translocase CDTb double mut... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28207 | |||||||||
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Title | Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A | |||||||||
Map data | ||||||||||
Sample |
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Keywords | translocase / binary toxin / calcium / TOXIN | |||||||||
Function / homology | Function and homology information protein homooligomerization / transferase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridioides difficile (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
Authors | Abeyawardhane DL / Pozharski E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Calcium-mediated Pore Formation of Clostridioides difficile Binary Toxin Authors: Abeyawardhane DL / Adipietro KA / Ruiz RG / Varney KM / Rustandi RR / Silin VI / Pozharski E / Weber DJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28207.map.gz | 125.3 MB | EMDB map data format | |
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Header (meta data) | emd-28207-v30.xml emd-28207.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28207_fsc.xml | 18.4 KB | Display | FSC data file |
Images | emd_28207.png | 115.3 KB | ||
Others | emd_28207_half_map_1.map.gz emd_28207_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28207 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28207 | HTTPS FTP |
-Validation report
Summary document | emd_28207_validation.pdf.gz | 1023.5 KB | Display | EMDB validaton report |
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Full document | emd_28207_full_validation.pdf.gz | 1023 KB | Display | |
Data in XML | emd_28207_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_28207_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28207 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28207 | HTTPS FTP |
-Related structure data
Related structure data | 8ekmMC 8ekkC 8eklC 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_28207.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.889 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28207_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28207_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Single heptamer of Clostridioides difficile binary toxin transloc...
Entire | Name: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant |
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Components |
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-Supramolecule #1: Single heptamer of Clostridioides difficile binary toxin transloc...
Supramolecule | Name: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Clostridioides difficile (bacteria) / Strain: R20291 |
-Macromolecule #1: ADP-ribosyltransferase binding component
Macromolecule | Name: ADP-ribosyltransferase binding component / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridioides difficile (bacteria) / Strain: R20291 |
Molecular weight | Theoretical: 74.591078 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: LMSDWEDEDL DTDNDNIPDS YERNGYTIKD LIAVKWEDSF AEQGYKKYVS NYLESNTAGD PYTDYEKASG SFDKAIKTEA RDPLVAAYP IVGVGMEKLI ISTNEHASTD QGKTVSRATT NSKTESNTAG VSVNVGYQNG FTANVTTNYS HTTDNSTAVQ D SNGESWNT ...String: LMSDWEDEDL DTDNDNIPDS YERNGYTIKD LIAVKWEDSF AEQGYKKYVS NYLESNTAGD PYTDYEKASG SFDKAIKTEA RDPLVAAYP IVGVGMEKLI ISTNEHASTD QGKTVSRATT NSKTESNTAG VSVNVGYQNG FTANVTTNYS HTTDNSTAVQ D SNGESWNT GLSINKGESA YINANVRYYN TGTAPMYKVT PTTNLVLDGD TLSTIKAQEN QIGNNLSPGD TYPKKGLSPL AL NTMDQFS SRLIPINYDQ LKKLDAGKQI KLETTQVSGN FGTKNSSGQI VTEGNSWSDY ISQIDSISAS IILDTENESY ERR VTAKNL QDPEDKTPEL TIGEAIEKAF GATKKDGLLY FNDIPIDESC VELIFDDNTA NKIKDSLKTL SDKKIYNVKL ERGM NILIK TPTYFTNFAD YNNYPSTWSN VNTTNQDGLQ GSANKLNGET KIKIPMSELK PYKRYVFSGY SKDPLTSNSI IVKIK AKEE KTDYLVPEQG YTKFSYEFET TEKDSSNIEI TLIGSGTTYL ANLSITELNS TPEILDEPEV KIPTDQEIMD AHKIYF ADL NFNPSTGNTY INGMYFAPTQ TNKEALDYIQ KYRVEATLQY SGFKDIGTKD KEMRNYLGDP NQPKTNYVNL RSYFTGG EN IMTYKKLRIY AITPDDRELL VLSVD UniProtKB: ADP-ribosyltransferase binding component |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 14 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |