+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30625 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Vibrio cholera aldehyde-alcohol dehrogenase | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Keywords | Enzyme / Fermentation / Alcohol / Aldehyde / OXIDOREDUCTASE | ||||||||||||
Function / homology | Function and homology information : / 3-chloroallyl aldehyde dehydrogenase activity / acetaldehyde dehydrogenase (acetylating) activity / fermentation / alcohol metabolic process / carbon utilization / alcohol dehydrogenase (NAD+) activity / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Vibrio cholerae (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.37 Å | ||||||||||||
Authors | Cho S / Cho C | ||||||||||||
Funding support | Korea, Republic Of, 3 items
| ||||||||||||
Citation | Journal: Biochem Biophys Res Commun / Year: 2021 Title: Cryo-EM structure of Vibrio cholerae aldehyde-alcohol dehydrogenase spirosomes. Authors: Saehyun Cho / Gijeong Kim / Ji-Joon Song / Carol Cho / Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it ...Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it is unknown whether AdhE structure is conserved in divergent bacteria. Here, we present the cryo-EM structure of AdhE (vAdhE) from Vibrio cholerae to 4.31 Å resolution. Overall, vAdhE spirosomes are similar to eAdhE with conserved subunit arrangement. However, divergences in key oligomerization residues cause vAdhE to form labile spirosomes with lower enzymatic activity. Mutating the vAdhE oligomerization interface to mimic eAdhE increases spirosome stability and enzymatic activity to levels comparable to eAdhE. These results support the generality of AdhE spirosome structures, and provide a structural basis to target vAdhE to attenuate bacterial virulence. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30625.map.gz | 73.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30625-v30.xml emd-30625.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_30625.png | 60 KB | ||
Filedesc metadata | emd-30625.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30625 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30625 | HTTPS FTP |
-Validation report
Summary document | emd_30625_validation.pdf.gz | 482.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30625_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | emd_30625_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_30625_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30625 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30625 | HTTPS FTP |
-Related structure data
Related structure data | 7dagMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30625.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.863 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Aldehyde-alcohol dehydrogenase spirosome
Entire | Name: Aldehyde-alcohol dehydrogenase spirosome |
---|---|
Components |
|
-Supramolecule #1: Aldehyde-alcohol dehydrogenase spirosome
Supramolecule | Name: Aldehyde-alcohol dehydrogenase spirosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Vibrio cholerae (bacteria) |
-Macromolecule #1: Aldehyde-alcohol dehydrogenase
Macromolecule | Name: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 96.346242 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPVTNLAELD ALVARVKAAQ AEFATFSQEQ VDKIFRAASL AANQARIPLA QMAVEESGMG IVEDKVIKNH FASEFIYNKY KDEKTCGIL EEDDNLGTMT IAEPVGIICG IVPTTNPTST AIFKSLISLK TRNGIIFSPH PRAKNSTNAA AKLVLDAAIA A GAPKDIIG ...String: MPVTNLAELD ALVARVKAAQ AEFATFSQEQ VDKIFRAASL AANQARIPLA QMAVEESGMG IVEDKVIKNH FASEFIYNKY KDEKTCGIL EEDDNLGTMT IAEPVGIICG IVPTTNPTST AIFKSLISLK TRNGIIFSPH PRAKNSTNAA AKLVLDAAIA A GAPKDIIG WIDQPSVELS NALMKHDGIA LILATGGPGM VKAAYSSGKP AIGVGAGNVP VVIDETADIK RAVASILMSK TF DNGVVCA SEQAAIVVSE VYDEVKERFA THKAHVLSKA DADKVRKVLL IDGALNAKIV GQPAAAIAEM AGVKVPADTK VLV GEGLGK VSYDDEFAHE KLSPTLGLFR ADNFEDAVAQ AVTMVEIGGI GHTSGLYTNQ DVNADRIRYF GDKLKTARIL VNIP TTHGG IGDLYNFNVA PSLTLGCGSW GGNSISENVG PKHLINKKTV AKRAENMLWH KLPKSIYFRR GSLPIALSDL EGKKR AFLV TDRFLFNNGY ADDVVALLKA QGMEVQTFFE VEADPTLSVV EKGAAAMQSF QPDVILALGG GSPMDAAKIM WVMYEH PDT HFEELAMRFM DIRKRIYKFP KMGKKAELVC ITTTSGTGSE VTPFAVVTDD KTGAKYPLAD YELTPQMAIV DANLVMN MP KSLTAFGGYD AVTHALEAYV SVLANEYSDG QALQALKMLK EYLPSSYANG AKDPIAREKV HNAATIAGIA FANAFLGV C HSMAHKIGAE FHLPHGLANA LLIANVVRYN ANDNPTKQTA FSQYDRPQAR RRYAEVADHL GLSQPGDRTA QKIERLLTW LDELKVNLDI PKSIQAAGVA EADFLAKVDE LAVEAFDDQC TGANPRYPLI AELKEVLLAS YYGKPFVEGQ TFEGTTVIVK KADQEAAKA PKAKK UniProtKB: Aldehyde-alcohol dehydrogenase |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62417 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |