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- EMDB-45091: Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pent... -
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Open data
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Basic information
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Title | Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila | |||||||||
![]() | Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila | |||||||||
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![]() | CO-dehydrogenase / acetyl-CoA synthase / Methanosarcina thermophila / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / acetyltransferase activity / iron-sulfur cluster binding / nickel cation binding ...methanogenesis, from acetate / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / acetyltransferase activity / iron-sulfur cluster binding / nickel cation binding / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Biester A / Drennan CL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy. Authors: Alison Biester / David A Grahame / Catherine L Drennan / ![]() Abstract: Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A- ...Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from (CODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our CODH/ACS structure with our CODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 18.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.2 KB 22.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 75 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 193.9 MB 193.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 986.4 KB | Display | ![]() |
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Full document | ![]() | 986 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9c0sMC ![]() 9c0qC ![]() 9c0rC ![]() 9c0tC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.654 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: Half Map B
File | emd_45091_half_map_1.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
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Density Histograms |
-Half map: Half Map A
File | emd_45091_half_map_2.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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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-#3 Details: Carbon monoxide dehydrogenase heterotetramer, alpha and epsilon subunits, with acetyl-CoA synthase beta subunit |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 265 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: ![]() ![]() |
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: ![]() ![]() |
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: Acetyl-CoA decarbonylase/synthase complex subunit beta 2
Macromolecule | Name: Acetyl-CoA decarbonylase/synthase complex subunit beta 2 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: CO-methylating acetyl-CoA synthase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 52.802227 KDa |
Sequence | String: MSEFPFEISP MFEGERVRKE GMFVELGGPK SLGLELVRAK PMDEIEDGKV TIVGPDLKDM EEGKTYPWAM IFHVGGELVE PDLESVIER RVHDFINYCQ GIMHLNQRYD VWMRISKDTA AKMDSFEPFG KAVMMLFKTE LPFIEKMQVT FYTDQAEVEK Q MAEAMEIF ...String: MSEFPFEISP MFEGERVRKE GMFVELGGPK SLGLELVRAK PMDEIEDGKV TIVGPDLKDM EEGKTYPWAM IFHVGGELVE PDLESVIER RVHDFINYCQ GIMHLNQRYD VWMRISKDTA AKMDSFEPFG KAVMMLFKTE LPFIEKMQVT FYTDQAEVEK Q MAEAMEIF KARDARTKDL HDEDVDVFYG CTLCQSFAPT NVCVVSPDRV SLCGAINWFD GRAAAKVDPE GPQFAIEKGE LL DAKTGEY SGVNEVAKKL SSGEFDKIKL HSFFDAPHTS CGCFEVVGFY IPEVDGIGWV NREYQGMAPN GLGFSTMAGQ TGG GKQIVG FLGIGINYFY SPKFIQADGG WNRVVWLPSM LKEKIDEAIP DDMKDKIATE KDVTDIESLK TFLKEKNHPV VANW AAEAE EEEEEEEEEE EVAAEAAPMM MPAAGFQMPA MPAMPMMSGG AGGIKLTFKN AKITIDRMII SEKKEKK UniProtKB: Acetyl-CoA decarbonylase/synthase complex subunit beta 2 |
-Macromolecule #4: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 8 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ![]() ChemComp-FS1: |
-Macromolecule #5: Fe(3)-Ni(1)-S(4) cluster
Macromolecule | Name: Fe(3)-Ni(1)-S(4) cluster / type: ligand / ID: 5 / Number of copies: 2 / Formula: RQM |
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Molecular weight | Theoretical: 410.333 Da |
Chemical component information | ![]() ChemComp-RQM: |
-Macromolecule #6: FE3-S4 CLUSTER
Macromolecule | Name: FE3-S4 CLUSTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: F3S |
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Molecular weight | Theoretical: 295.795 Da |
Chemical component information | ![]() ChemComp-F3S: |
-Macromolecule #7: CARBON MONOXIDE
Macromolecule | Name: CARBON MONOXIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: CMO |
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Molecular weight | Theoretical: 28.01 Da |
Chemical component information | ![]() ChemComp-CMO: |
-Macromolecule #8: NICKEL (II) ION
Macromolecule | Name: NICKEL (II) ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: NI |
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Molecular weight | Theoretical: 58.693 Da |
Chemical component information | ![]() ChemComp-NI: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.2 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 82 % / Chamber temperature: 298 K / Details: SPT Labtech chameleon plunger. |
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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: 47.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 130000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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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: 76.1221 / Target criteria: Correlation coefficient |
Output model | ![]() PDB-9c0s: |