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Yorodumi- EMDB-28205: Clostridioides difficile binary toxin translocase CDTb wild-type ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28205 | |||||||||
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Title | Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | translocase / binary toxin / pore-forming / TOXIN | |||||||||
Function / homology | Function and homology information protein homooligomerization / transferase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridioides difficile (bacteria) / Clostridioides difficile R20291 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 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_28205.map.gz | 55.4 MB | EMDB map data format | |
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Header (meta data) | emd-28205-v30.xml emd-28205.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28205_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_28205.png | 127.2 KB | ||
Others | emd_28205_half_map_1.map.gz emd_28205_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28205 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28205 | HTTPS FTP |
-Related structure data
Related structure data | 8ekkMC 8eklC 8ekmC 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_28205.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_28205_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28205_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Single heptamer (class 2) of Clostridioides difficile binary toxi...
Entire | Name: Single heptamer (class 2) of Clostridioides difficile binary toxin translocase CDTb wilt-type after depletion of calcium from RBD1 |
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Components |
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-Supramolecule #1: Single heptamer (class 2) of Clostridioides difficile binary toxi...
Supramolecule | Name: Single heptamer (class 2) of Clostridioides difficile binary toxin translocase CDTb wilt-type after depletion of calcium from RBD1 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 R20291 (bacteria) / Strain: R20291 |
Molecular weight | Theoretical: 74.679086 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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 TPTYFTNFDD YNNYPSTWSN VNTTNQDGLQ GSANKLNGET KIKIPMSELK PYKRYVFSGY SKDPLTSNSI IVKIK AKEE KTDYLVPEQG YTKFSYEFET TEKDSSNIEI TLIGSGTTYL DNLSITELNS 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 |