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Yorodumi- EMDB-17583: CHAPSO treated partial catalytic component (comprising only AnfD ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17583 | |||||||||
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Title | CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus | |||||||||
Map data | Core complex of Fe-nitrogenase comprising only AnfD and AnfK. | |||||||||
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 / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodobacter capsulatus SB 1003 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 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_17583.map.gz | 122.2 MB | EMDB map data format | |
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Header (meta data) | emd-17583-v30.xml emd-17583.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17583_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_17583.png | 59.8 KB | ||
Filedesc metadata | emd-17583.cif.gz | 6.3 KB | ||
Others | emd_17583_half_map_1.map.gz emd_17583_half_map_2.map.gz | 120.1 MB 120.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17583 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17583 | HTTPS FTP |
-Related structure data
Related structure data | 8pbbMC 8oieC 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_17583.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Core complex of Fe-nitrogenase comprising only AnfD and AnfK. | ||||||||||||||||||||
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: half-map A
File | emd_17583_half_map_1.map | ||||||||||||
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Annotation | half-map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map B
File | emd_17583_half_map_2.map | ||||||||||||
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Annotation | half-map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CHAPSO treated partial catalytic component (comprising only AnfD ...
Entire | Name: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus |
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Components |
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-Supramolecule #1: CHAPSO treated partial catalytic component (comprising only AnfD ...
Supramolecule | Name: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Rhodobacter capsulatus SB 1003 (bacteria) |
-Macromolecule #1: Nitrogenase protein alpha chain
Macromolecule | Name: Nitrogenase protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rhodobacter capsulatus SB 1003 (bacteria) |
Molecular weight | Theoretical: 60.221117 KDa |
Recombinant expression | Organism: Rhodobacter capsulatus SB 1003 (bacteria) |
Sequence | String: MPYHEFEVSK CIPERREHAV MKAAGEDLTS CLPKGYLNTI PGTISERGCA YCGAKHVIGT PMKDVIHISH GPNGCTYDTW QTKRYISDN DNFQLKYTFA TDVKEKHVVF GAEGLLKKSM HEAFDAFPNI KRMTVYQTCT TALIGDDVDA IAKEVMEERG D VDVFVCNS ...String: MPYHEFEVSK CIPERREHAV MKAAGEDLTS CLPKGYLNTI PGTISERGCA YCGAKHVIGT PMKDVIHISH GPNGCTYDTW QTKRYISDN DNFQLKYTFA TDVKEKHVVF GAEGLLKKSM HEAFDAFPNI KRMTVYQTCT TALIGDDVDA IAKEVMEERG D VDVFVCNS PGFAGPSQSG GHHKINIAWL NQKVGTVEPD YLGEHVINYV GEYNIQGDQE VMIDYFNRMG IQVLSTFTGN GS YDSLRMM HRAHLNVLEC ARSAEYICDE LRARYGIPRL DIDGFGFEPL ANSLRKVALF FGIEDKAEAI IAEEYAKWKP QLD WYKERL KGKKVCLWPG GSKLWHWAHA IEEEMGLKVV SVYTKFGHQG DMEKGVSRCG EGALAIDDPN ELESVEAIEM LKPD IIFTG KRPGEFVKKH GVPYLNAHAY HNGPYKGFEG WVRFARDIYN AIYSPMRQLA ALDISAPDAA ITSGFRTAKM NADLT VSDE VKFSEVLHEY TGKYDSIAEI RARNQAYAAE QKALRDAVQP AAEWSHPQFE K UniProtKB: Nitrogenase protein alpha chain |
-Macromolecule #2: Nitrogenase iron-iron protein, beta subunit
Macromolecule | Name: Nitrogenase iron-iron protein, beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase |
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Source (natural) | Organism: Rhodobacter capsulatus SB 1003 (bacteria) |
Molecular weight | Theoretical: 50.776398 KDa |
Recombinant expression | Organism: Rhodobacter capsulatus SB 1003 (bacteria) |
Sequence | String: MTCQVTQKAR EGTINPIFTC QPAGAQFASI GIKDCIGIVH GGQGCVMFVR LLISQHMKES FEIASSSVHE DGAVFGALDR VETAVEVLL TRYPDVKVVP IITTCSTEII GDDVDGLLSK LEDELLPTKF PGREVHLLTV HCPSFVGSMI TGYDKAVHDF V KKFATKDE ...String: MTCQVTQKAR EGTINPIFTC QPAGAQFASI GIKDCIGIVH GGQGCVMFVR LLISQHMKES FEIASSSVHE DGAVFGALDR VETAVEVLL TRYPDVKVVP IITTCSTEII GDDVDGLLSK LEDELLPTKF PGREVHLLTV HCPSFVGSMI TGYDKAVHDF V KKFATKDE PSDKINLITG WVNPGDVKEL KHLLEVMEVK ANVLFEVESF DSPLMPDLEH HSHGSTTIED LRDTANAKGT IA LNRYEGM KAADYLKKKF KVPAVIGPTP VGIRNTDAFL KAVSEMTGQP IPAQLVKERG LALDAIADIG HMFLADKRVA IYA NPDLAI GLTEFCLDLE MKPKLLLLGD DNSGYVKDPR VLALQENAPD LEIVTNADFW DLESRIQQGL ELDLILGHSK GRFI SIDYK VPMVRVGFPT YDRAGMYRHP VLGYGGAMFL AETMANTLFA DMEAKKNKEW ILNVW UniProtKB: Nitrogenase iron-iron protein, beta subunit |
-Macromolecule #3: FE(8)-S(7) CLUSTER
Macromolecule | Name: FE(8)-S(7) CLUSTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLF |
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Molecular weight | Theoretical: 671.215 Da |
Chemical component information | ChemComp-CLF: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL |
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Buffer | pH: 7.8 Details: 37.5 mM TRIS (pH = 7.8) 150 mM NaCl 3.75 mM sodium dithionite 0.4 % (m/V) CHAPSO |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 281 K / 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 / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |