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Yorodumi- EMDB-26756: C1 symmetric cryoEM structure of Azotobacter vinelandii MoFeP und... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26756 | |||||||||||||||
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Title | C1 symmetric cryoEM structure of Azotobacter vinelandii MoFeP under non-turnover conditions | |||||||||||||||
Map data | sharpened map | |||||||||||||||
Sample |
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Keywords | nitrogenase / MoFeP / nitrogen fixation / OXIDOREDUCTASE | |||||||||||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Azotobacter vinelandii DJ (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.91 Å | |||||||||||||||
Authors | Rutledge HL / Cook B / Tezcan FA / Herzik MA | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Science / Year: 2022 Title: Structures of the nitrogenase complex prepared under catalytic turnover conditions. Authors: Hannah L Rutledge / Brian D Cook / Hoang P M Nguyen / Mark A Herzik / F Akif Tezcan / Abstract: The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ...The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here, we report cryo-electron microscopy structures of the nitrogenase complex prepared under enzymatic turnover conditions. We observe that asymmetry governs all aspects of the nitrogenase mechanism, including ATP hydrolysis, protein-protein interactions, and catalysis. Conformational changes near the catalytic iron-molybdenum cofactor are correlated with the nucleotide-hydrolysis state of the enzyme. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26756.map.gz | 484.4 MB | EMDB map data format | |
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Header (meta data) | emd-26756-v30.xml emd-26756.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26756_fsc.xml | 16.8 KB | Display | FSC data file |
Images | emd_26756.png | 121.9 KB | ||
Masks | emd_26756_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-26756.cif.gz | 6.9 KB | ||
Others | emd_26756_additional_1.map.gz emd_26756_half_map_1.map.gz emd_26756_half_map_2.map.gz | 258.4 MB 474.7 MB 474.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26756 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26756 | HTTPS FTP |
-Validation report
Summary document | emd_26756_validation.pdf.gz | 994.1 KB | Display | EMDB validaton report |
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Full document | emd_26756_full_validation.pdf.gz | 993.7 KB | Display | |
Data in XML | emd_26756_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | emd_26756_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26756 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26756 | HTTPS FTP |
-Related structure data
Related structure data | 7ut6MC 7ut7C 7ut8C 7ut9C 7utaC 8dpnC 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_26756.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.815 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26756_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_26756_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: gold-standard half map B
File | emd_26756_half_map_1.map | ||||||||||||
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Annotation | gold-standard half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: gold-standard half map A
File | emd_26756_half_map_2.map | ||||||||||||
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Annotation | gold-standard half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heterotetrameric MoFeP from Azotobacter vinelandii
Entire | Name: Heterotetrameric MoFeP from Azotobacter vinelandii |
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Components |
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-Supramolecule #1: Heterotetrameric MoFeP from Azotobacter vinelandii
Supramolecule | Name: Heterotetrameric MoFeP from Azotobacter vinelandii / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Wild-type MoFeP was purified from the native organism, Azotobacter vinelandii |
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Source (natural) | Organism: Azotobacter vinelandii DJ (bacteria) |
Molecular weight | Theoretical: 233.21 KDa |
-Macromolecule #1: Nitrogenase molybdenum-iron protein alpha chain
Macromolecule | Name: Nitrogenase molybdenum-iron protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase |
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Source (natural) | Organism: Azotobacter vinelandii DJ (bacteria) |
Molecular weight | Theoretical: 55.363043 KDa |
Sequence | String: MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK KSQPGLMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEVE TLFPLNKGIS VQSECPIGLI G DDIESVSK ...String: MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK KSQPGLMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEVE TLFPLNKGIS VQSECPIGLI G DDIESVSK VKGAELSKTI VPVRCEGFRG VSQSLGHHIA NDAVRDWVLG KRDEDTTFAS TPYDVAIIGD YNIGGDAWSS RI LLEEMGL RCVAQWSGDG SISEIELTPK VKLNLVHCYR SMNYISRHME EKYGIPWMEY NFFGPTKTIE SLRAIAAKFD ESI QKKCEE VIAKYKPEWE AVVAKYRPRL EGKRVMLYIG GLRPRHVIGA YEDLGMEVVG TGYEFAHNDD YDRTMKEMGD STLL YDDVT GYEFEEFVKR IKPDLIGSGI KEKFIFQKMG IPFREMHSWD YSGPYHGFDG FAIFARDMDM TLNNPCWKKL QAPWE ASEG AEKVAASA UniProtKB: Nitrogenase molybdenum-iron protein alpha chain |
-Macromolecule #2: Nitrogenase molybdenum-iron protein beta chain
Macromolecule | Name: Nitrogenase molybdenum-iron protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase |
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Source (natural) | Organism: Azotobacter vinelandii DJ (bacteria) |
Molecular weight | Theoretical: 59.535879 KDa |
Sequence | String: MSQQVDKIKA SYPLFLDQDY KDMLAKKRDG FEEKYPQDKI DEVFQWTTTK EYQELNFQRE ALTVNPAKAC QPLGAVLCAL GFEKTMPYV HGSQGCVAYF RSYFNRHFRE PVSCVSDSMT EDAAVFGGQQ NMKDGLQNCK ATYKPDMIAV STTCMAEVIG D DLNAFINN ...String: MSQQVDKIKA SYPLFLDQDY KDMLAKKRDG FEEKYPQDKI DEVFQWTTTK EYQELNFQRE ALTVNPAKAC QPLGAVLCAL GFEKTMPYV HGSQGCVAYF RSYFNRHFRE PVSCVSDSMT EDAAVFGGQQ NMKDGLQNCK ATYKPDMIAV STTCMAEVIG D DLNAFINN SKKEGFIPDE FPVPFAHTPS FVGSHVTGWD NMFEGIARYF TLKSMDDKVV GSNKKINIVP GFETYLGNFR VI KRMLSEM GVGYSLLSDP EEVLDTPADG QFRMYAGGTT QEEMKDAPNA LNTVLLQPWH LEKTKKFVEG TWKHEVPKLN IPM GLDWTD EFLMKVSEIS GQPIPASLTK ERGRLVDMMT DSHTWLHGKR FALWGDPDFV MGLVKFLLEL GCEPVHILCH NGNK RWKKA VDAILAASPY GKNATVYIGK DLWHLRSLVF TDKPDFMIGN SYGKFIQRDT LHKGKEFEVP LIRIGFPIFD RHHLH RSTT LGYEGAMQIL TTLVNSILER LDEETRGMQA TDYNHDLVR UniProtKB: Nitrogenase molybdenum-iron protein beta chain |
-Macromolecule #3: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
Macromolecule | Name: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: HCA |
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Molecular weight | Theoretical: 206.15 Da |
Chemical component information | ChemComp-HCA: |
-Macromolecule #4: iron-sulfur-molybdenum cluster with interstitial carbon
Macromolecule | Name: iron-sulfur-molybdenum cluster with interstitial carbon type: ligand / ID: 4 / Number of copies: 2 / Formula: ICS |
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Molecular weight | Theoretical: 787.451 Da |
Chemical component information | ChemComp-ICE: |
-Macromolecule #5: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #6: FE(8)-S(7) CLUSTER
Macromolecule | Name: FE(8)-S(7) CLUSTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: CLF |
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Molecular weight | Theoretical: 671.215 Da |
Chemical component information | ChemComp-CLF: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 415 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.44 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: Solutions were prepared and filtered immediately prior to the experiment. | |||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: Custom manual plunger. Greater than 95% humidity.. | |||||||||
Details | 1.44 mg/mL MoFeP |
-Electron microscopy
Microscope | TFS KRIOS |
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Temperature | Min: 93.0 K / Max: 123.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 3773 / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |