+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16890 | |||||||||
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Title | Iron Nitrogenase Complex from Rhodobacter capsulatus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nitrogen fixation / Fe nitrogenase / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodobacter capsulatus SB 1003 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||
Authors | Schmidt FV / Schulz L / Zarzycki J / Prinz S / Erb TJ / Rebelein JG | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural insights into the iron nitrogenase complex. Authors: Frederik V Schmidt / Luca Schulz / Jan Zarzycki / Simone Prinz / Niels N Oehlmann / Tobias J Erb / Johannes G Rebelein / Abstract: Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide ...Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [FeSC-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16890.map.gz | 108 MB | EMDB map data format | |
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Header (meta data) | emd-16890-v30.xml emd-16890.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16890_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_16890.png | 45.1 KB | ||
Filedesc metadata | emd-16890.cif.gz | 6.9 KB | ||
Others | emd_16890_half_map_1.map.gz emd_16890_half_map_2.map.gz | 193.8 MB 193.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16890 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16890 | HTTPS FTP |
-Related structure data
Related structure data | 8oieMC 8pbbC 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_16890.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_16890_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16890_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Iron Nitrogenase Complex from Rhodobacter capsulatus
+Supramolecule #1: Iron Nitrogenase Complex from Rhodobacter capsulatus
+Macromolecule #1: Nitrogenase protein alpha chain
+Macromolecule #2: Nitrogenase iron-iron protein delta chain
+Macromolecule #3: Nitrogenase iron-iron protein, beta subunit
+Macromolecule #4: Nitrogenase iron protein
+Macromolecule #5: FeFe cofactor
+Macromolecule #6: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
+Macromolecule #7: FE(8)-S(7) CLUSTER
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ALUMINUM FLUORIDE
+Macromolecule #11: IRON/SULFUR CLUSTER
+Macromolecule #12: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 Details: 50 mM TRIS (pH = 7.8) 200 mM NaCl 5 mM sodium dithionite |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN 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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |