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Yorodumi- EMDB-10495: Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10495 | ||||||||||||
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Title | Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | molybdoenzyme / formate oxidation / NAD+-dependent / OXIDOREDUCTASE | ||||||||||||
Function / homology | Function and homology information formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding ...formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | ||||||||||||
Authors | Wendler P / Radon C | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Authors: Christin Radon / Gerd Mittelstädt / Benjamin R Duffus / Jörg Bürger / Tobias Hartmann / Thorsten Mielke / Christian Teutloff / Silke Leimkühler / Petra Wendler / Abstract: Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor ...Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10495.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-10495-v30.xml emd-10495.xml | 21 KB 21 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10495_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_10495.png | 93 KB | ||
Filedesc metadata | emd-10495.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10495 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10495 | HTTPS FTP |
-Validation report
Summary document | emd_10495_validation.pdf.gz | 431.5 KB | Display | EMDB validaton report |
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Full document | emd_10495_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | emd_10495_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_10495_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10495 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10495 | HTTPS FTP |
-Related structure data
Related structure data | 6tg9MC 6tgaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10495.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Formate dehydrogenase, NADH reduced
+Supramolecule #1: Formate dehydrogenase, NADH reduced
+Macromolecule #1: Formate dehydrogenase subunit alpha
+Macromolecule #2: Formate dehydrogenase subunit beta
+Macromolecule #3: Formate dehydrogenase subunit gamma
+Macromolecule #4: NAD-dependent formate dehydrogenase subunit delta
+Macromolecule #5: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...
+Macromolecule #6: MOLYBDENUM(VI) ION
+Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #8: IRON/SULFUR CLUSTER
+Macromolecule #9: HYDROSULFURIC ACID
+Macromolecule #10: FLAVIN MONONUCLEOTIDE
+Macromolecule #11: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI POLARA 300 |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (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
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: BACKBONE TRACE | ||||||||
Output model | PDB-6tg9: |