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Open data
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Basic information
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Title | CryoEM structure of ancestral nitrogenase MoFe-protein | |||||||||
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![]() | Metalloprotein / OXIDOREDUCTASE | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.19 Å | |||||||||
![]() | Shen Y / Warmack RA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes. Authors: Yuanbo Shen / Ailiena O Maggiolo / Tianzheng Zhang / Rebeccah A Warmack / ![]() Abstract: Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry ...Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 684.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19 KB | Display | ![]() |
Images | ![]() | 104.3 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 677.1 MB 677.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 985 KB | Display | ![]() |
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Full document | ![]() | 984.6 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9nsvMC ![]() 9n4vC ![]() 9n4wC ![]() 9n4xC ![]() 9n4yC ![]() 9n59C ![]() 9n5aC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_49753_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_49753_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nitrogenase MoFe-protein
Entire | Name: Nitrogenase MoFe-protein |
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Components |
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-Supramolecule #1: Nitrogenase MoFe-protein
Supramolecule | Name: Nitrogenase MoFe-protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Nitrogenase MoFe-protein alpha chain
Macromolecule | Name: Nitrogenase MoFe-protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.73318 KDa |
Sequence | String: MTGMSRDEVE SLIQEVLEVY PEKAKKNREK HLSPNDPELE QSKKCITSNK KSLPGVMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEIE TLFPLNKGIS VQSECPIGLI G DDIEAVSK ...String: MTGMSRDEVE SLIQEVLEVY PEKAKKNREK HLSPNDPELE QSKKCITSNK KSLPGVMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEIE TLFPLNKGIS VQSECPIGLI G DDIEAVSK QKGKEHGKTI VPVRCEGFRG VSQSLGHHIA NDAVRDWVLS ARDDDDSFET TDYDVAIIGD YNIGGDAWSS RI LLEEMGL RVVAQWSGDG TISEMELTPK VKLNLVHCYR SMNYISRHME EKYGIPWMEY NFFGPTKTIE SLRKIAAQFD ESI QKKCEE VIAKYQPEWE AVVAKYRPRL EGKRVMLYVG GLRPRHVIGA YEDLGMEVVG TGYEFGHNDD YDRTLKEMGD STLL YDDVT GYEFEEFVKK VKPDLIGSGI KEKYIFQKMG IPFRQMHSWD YSGPYHGFDG FAIFARDMDM TLNNPCWKKL QAPWK KSEQ ADEAVAASA |
-Macromolecule #2: Nitrogenase MoFe-protein beta chain
Macromolecule | Name: Nitrogenase MoFe-protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.071207 KDa |
Sequence | String: MSQQVDNIKP SYPLFRDQDY KDMLAKKRDN FEEKHPQEKI DEVFQWTTTE EYQELNFQRE ALTVNPAKAC QPLGAVLCSL GFEKTMPYV HGSQGCVAYF RTYFNRHFKE PISCVSDSMT EDAAVFGGQQ NMKDGLQNCK AIYKPDMIAV STTCMAEVIG D DLNAFINN ...String: MSQQVDNIKP SYPLFRDQDY KDMLAKKRDN FEEKHPQEKI DEVFQWTTTE EYQELNFQRE ALTVNPAKAC QPLGAVLCSL GFEKTMPYV HGSQGCVAYF RTYFNRHFKE PISCVSDSMT EDAAVFGGQQ NMKDGLQNCK AIYKPDMIAV STTCMAEVIG D DLNAFINN SKKEGHIPDE FPVPFAHTPS FVGSHVTGWD NMFEGIARYF TLNYMEDKEV GSNGKINIVP GFETYLGNFR VI KRMMNEM NVDYTLLSDP EEVLDTPADG QFRMYAGGTT QDEMKDAPNA LNTLMLQPWQ LTKTTKFVKN TWKHEVPKLN IPM GLDWTD EFLMKVSEIS GQPIPESLAK ERGRLVDMMT DSHTWLHGKK FALWGDPDFV MGMTKFLLEL GCEPIHILCN NANK RWKKA MDAILAESPY GANSEVHIGK DLWHMRSLVF TNKPDFMIGN SYGKFIQRDT LYKGKEFEVP LIRIGFPIFD RHHLH RQTT LGYEGAMQIL TTLVNSVLER LDEETRGMQT TDYNYDLVR |
-Macromolecule #3: iron-sulfur-molybdenum cluster with interstitial carbon
Macromolecule | Name: iron-sulfur-molybdenum cluster with interstitial carbon type: ligand / ID: 3 / Number of copies: 2 / Formula: ICS |
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Molecular weight | Theoretical: 787.451 Da |
Chemical component information | ![]() ChemComp-ICE: |
-Macromolecule #4: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
Macromolecule | Name: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: HCA |
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Molecular weight | Theoretical: 206.15 Da |
Chemical component information | ![]() ChemComp-HCA: |
-Macromolecule #5: FE(8)-S(7) CLUSTER
Macromolecule | Name: FE(8)-S(7) CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLF |
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Molecular weight | Theoretical: 671.215 Da |
Chemical component information | ![]() ChemComp-CLF: |
-Macromolecule #6: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 1394 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |