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Yorodumi- EMDB-20692: Structure of the membrane-bound sulfane sulfur reductase (MBS), a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20692 | |||||||||
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Title | Structure of the membrane-bound sulfane sulfur reductase (MBS), an archaeal respiratory membrane complex | |||||||||
Map data | structure of an archaea respiratory membrane complex | |||||||||
Sample |
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Keywords | cryoEM / membrane protein / respiratory system | |||||||||
Function / homology | Function and homology information NADH dehydrogenase (quinone) / : / monoatomic ion transmembrane transporter activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase (ubiquinone) activity / quinone binding / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 ...NADH dehydrogenase (quinone) / : / monoatomic ion transmembrane transporter activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase (ubiquinone) activity / quinone binding / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Pyrococcus furiosus (archaea) / Pyrococcus furiosus COM1 (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Yu HJ / Li HL | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life. Authors: Hongjun Yu / Dominik K Haja / Gerrit J Schut / Chang-Hao Wu / Xing Meng / Gongpu Zhao / Huilin Li / Michael W W Adams / Abstract: Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas- ...Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S)-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20692.map.gz | 115.3 MB | EMDB map data format | |
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Header (meta data) | emd-20692-v30.xml emd-20692.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20692_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_20692.png | 52.8 KB | ||
Filedesc metadata | emd-20692.cif.gz | 7.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20692 | HTTPS FTP |
-Validation report
Summary document | emd_20692_validation.pdf.gz | 580.2 KB | Display | EMDB validaton report |
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Full document | emd_20692_full_validation.pdf.gz | 579.8 KB | Display | |
Data in XML | emd_20692_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_20692_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20692 | HTTPS FTP |
-Related structure data
Related structure data | 6u8yMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | structure of an archaea respiratory membrane complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.029 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : respiratory membrane complex
+Supramolecule #1: respiratory membrane complex
+Macromolecule #1: Monovalent cation/H+ antiporter subunit E
+Macromolecule #2: Monovalent cation/H+ antiporter subunit F
+Macromolecule #3: Monovalent cation/H+ antiporter subunit G
+Macromolecule #4: DUF4040 domain-containing protein
+Macromolecule #5: Monovalent cation/H+ antiporter subunit B
+Macromolecule #6: Monovalent cation/H+ antiporter subunit C
+Macromolecule #7: NADH dehydrogenase subunit N
+Macromolecule #8: NADH dehydrogenase subunit M
+Macromolecule #9: NADH dehydrogenase subunit B
+Macromolecule #10: NADH dehydrogenase subunit C
+Macromolecule #11: NADH dehydrogenase subunit D
+Macromolecule #12: NADH dehydrogenase subunit
+Macromolecule #13: NADH dehydrogenase subunit I
+Macromolecule #14: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |