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Yorodumi- EMDB-45089: Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermoph... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45089 | |||||||||
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Title | Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on blot plunger | |||||||||
Map data | Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on blot plunger | |||||||||
Sample |
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Keywords | CO-dehydrogenase / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information methanogenesis, from acetate / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / nickel cation binding / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | |||||||||
Biological species | Methanosarcina thermophila (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Biester A / Drennan CL | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy. Authors: Biester A / Grahame DA / Drennan CL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45089.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-45089-v30.xml emd-45089.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45089_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_45089.png | 67.4 KB | ||
Masks | emd_45089_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-45089.cif.gz | 6.6 KB | ||
Others | emd_45089_half_map_1.map.gz emd_45089_half_map_2.map.gz | 48.6 MB 48.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45089 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45089 | HTTPS FTP |
-Validation report
Summary document | emd_45089_validation.pdf.gz | 740.4 KB | Display | EMDB validaton report |
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Full document | emd_45089_full_validation.pdf.gz | 740 KB | Display | |
Data in XML | emd_45089_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_45089_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45089 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45089 | HTTPS FTP |
-Related structure data
Related structure data | 9c0qMC 9c0rC 9c0sC 9c0tC C: citing same article (ref.) M: atomic model generated by this map |
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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_45089.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on blot plunger | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.17 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_45089_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_45089_half_map_1.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_45089_half_map_2.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Acetyl-CoA decarbonylase/synthase complex
Entire | Name: Acetyl-CoA decarbonylase/synthase complex |
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Components |
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-Supramolecule #1: Acetyl-CoA decarbonylase/synthase complex
Supramolecule | Name: Acetyl-CoA decarbonylase/synthase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Carbon monoxide dehydrogenase heterotetramer, alpha and epsilon subunits |
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Source (natural) | Organism: Methanosarcina thermophila (archaea) |
Molecular weight | Theoretical: 212 KDa |
-Macromolecule #1: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2
Macromolecule | Name: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: anaerobic carbon monoxide dehydrogenase |
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Source (natural) | Organism: Methanosarcina thermophila (archaea) |
Molecular weight | Theoretical: 87.855852 KDa |
Sequence | String: MSKLTTGSFS IEDLESVQIT INNIVGAAKE AAEKAEEELG PMGPTPFPTA ATVRDWSFTL FDRYEPVYTP MCDQCCYCTF GPCNLEGNR RGACGLDMKG QAAREFFLRC ITGCACHSAH GRHLLDHIIS IFGEDMPINM GASNVIAPNI QLITGRQPKT L GDLKPIME ...String: MSKLTTGSFS IEDLESVQIT INNIVGAAKE AAEKAEEELG PMGPTPFPTA ATVRDWSFTL FDRYEPVYTP MCDQCCYCTF GPCNLEGNR RGACGLDMKG QAAREFFLRC ITGCACHSAH GRHLLDHIIS IFGEDMPINM GASNVIAPNI QLITGRQPKT L GDLKPIME YVEEELGQLL ATVHAGQEGA AIDYDNKAML AGILDHVGME VSDIAQVTAL GFPKSDPEAP LVEVGMGTLD AS KPVIIAI GHNVAGVTYI MDYMEDNNLT DKMEIGGLCC TAFDMTRYKR EDRKPPYAKI VGTISKELKV VRSGIPDVIV IDE QCVRAD LVEEGKKLKI PVIASNEKVM YGLPDRTNDD VDAIIEDIKT GKIPGCVMLD YEKLGELVPR LAMEMAPLRE GISA IPSDE EMASLVAKCV ACGECALACP EELDIPDAIQ AAKEGDFTAL DFLHDLCVGC RRCEQVCNKE IPILSVIDKA AQKAI AEEK GLVRAGRGQV SDAEIRAEGL NLVMGTTPGV IAIIGCANYP AGSKDVYRIA EEFLNRNYIV AVSGCSAMDI GMYKDA DGK TLYERFPGRF ERGNILNTGS CVSNSHISGT CHKVAAIFAG RNLSGNLAEI ADYTLNRVGA VGLAWGAYSQ KAAAIGT GC NMYGIPAVLG PHSGKYRRAL IAKTYDENKW KVYDSRNGSE LDIPPSPEFL ITTAETWQEA CVLLAKNCIR PSDNNMGR S IKLTHWIELS EKYLGVLPED WWKFVRHEAD LPLSRREELL KKLETEHGWE IDWKKKKIIS GPKIKFDVSS QPTNLKRLC KEA UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit alpha 2 |
-Macromolecule #2: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2
Macromolecule | Name: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Methanosarcina thermophila (archaea) |
Molecular weight | Theoretical: 18.587375 KDa |
Sequence | String: MVDTTKNTKL FTSYGVKTSK AITTEVAAKL ISKAKRPLFV VGTGVLDPEL LDRAVKIAKA KNIPIAATGS SMPGFVDKDV NAKYINLHQ LGFYLTDPDW PGLDGNGNYD TIILLGHKKY YINQVLSAVK NFSDVKSISI DRNYIQNATM SFGNLSKADH I AALDEVID LL UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2 |
-Macromolecule #3: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 3 / Number of copies: 7 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Macromolecule #4: Fe(3)-Ni(1)-S(4) cluster
Macromolecule | Name: Fe(3)-Ni(1)-S(4) cluster / type: ligand / ID: 4 / Number of copies: 2 / Formula: RQM |
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Molecular weight | Theoretical: 410.333 Da |
Chemical component information | ChemComp-RQM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Software | Name: EPU |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.53 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Software | Name: Coot (ver. 0.9.8.92) |
Details | Initial model was generated using AlphaFold, fit to the map using ChimeraX, followed by rigid body fitting in phenix, and finally iterative real space refinement in coot and phenix. |
Refinement | Space: REAL / Overall B value: 90.5204 / Target criteria: Correlation coefficient |
Output model | PDB-9c0q: |