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Yorodumi- PDB-8q3v: Cryo-EM structure of the methanogenic Na+ translocating N5-methyl... -
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-Basic information
Entry | Database: PDB / ID: 8q3v | ||||||
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Title | Cryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex | ||||||
Components | (Tetrahydromethanopterin S-methyltransferase subunit ...) x 7 | ||||||
Keywords | TRANSFERASE / methanogenesis / tetrahydromethanopterin / coenzyme M / vitamin B12 / Na+ transport | ||||||
Function / homology | Function and homology information tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methyltransferase complex / methanogenesis, from carbon dioxide / vesicle membrane / cobalt ion binding / sodium ion transport / one-carbon metabolic process / methylation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Methanothermobacter marburgensis (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.08 Å | ||||||
Authors | Aziz, I. / Vonck, J. / Ermler, U. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Authors: Iram Aziz / Kanwal Kayastha / Susann Kaltwasser / Janet Vonck / Sonja Welsch / Bonnie J Murphy / Jörg Kahnt / Di Wu / Tristan Wagner / Seigo Shima / Ulrich Ermler / Abstract: Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy ...Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by -methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG) composed of the central Mtr(ABFG) stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B-carrying domain. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q3v.cif.gz | 614.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q3v.ent.gz | 499.7 KB | Display | PDB format |
PDBx/mmJSON format | 8q3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q3v_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8q3v_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8q3v_validation.xml.gz | 99.3 KB | Display | |
Data in CIF | 8q3v_validation.cif.gz | 149.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/8q3v ftp://data.pdbj.org/pub/pdb/validation_reports/q3/8q3v | HTTPS FTP |
-Related structure data
Related structure data | 18135MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Tetrahydromethanopterin S-methyltransferase subunit ... , 7 types, 21 molecules AaQBbRCcSDdTEeUFfVGgW
#1: Protein | Mass: 25640.320 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: P80184 #2: Protein | Mass: 10725.471 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: Q59584 #3: Protein | Mass: 27132.244 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: P80185 #4: Protein | Mass: 22783.881 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: P80183 #5: Protein | Mass: 31253.289 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: P80186 #6: Protein | Mass: 7325.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: Q50773 #7: Protein | Mass: 9519.042 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis (archaea) References: UniProt: Q50774 |
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-Non-polymers , 4 types, 229 molecules
#8: Chemical | #9: Chemical | ChemComp-JCV / [( Mass: 1706.543 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C98H193O19P #10: Chemical | ChemComp-NA / #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Methyl-H4MPT:CoM methyltransferase / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL |
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Molecular weight | Value: 430 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Methanothermobacter marburgensis (archaea) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 73.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138464 / Symmetry type: POINT | ||||||||||||||||||||||||
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