+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7468 | |||||||||
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Title | cryoEM structure of a respiratory membrane-bound hydrogenase | |||||||||
Map data | cryoEM structure of a respiratory membrane-bound hydrogenase | |||||||||
Sample |
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Keywords | respiratory / hydrogenase / ion translocation / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information : / monoatomic ion transmembrane transporter activity / ferredoxin hydrogenase / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / oxidoreductase activity, acting on NAD(P)H / monoatomic cation transmembrane transporter activity / proton motive force-driven ATP synthesis / nickel cation binding / NADH dehydrogenase (ubiquinone) activity ...: / monoatomic ion transmembrane transporter activity / ferredoxin hydrogenase / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / oxidoreductase activity, acting on NAD(P)H / monoatomic cation transmembrane transporter activity / proton motive force-driven ATP synthesis / nickel cation binding / 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) / Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Li HL / Yu HJ | |||||||||
Citation | Journal: Cell / Year: 2018 Title: Structure of an Ancient Respiratory System. Authors: Hongjun Yu / Chang-Hao Wu / Gerrit J Schut / Dominik K Haja / Gongpu Zhao / John W Peters / Michael W W Adams / Huilin Li / Abstract: Hydrogen gas-evolving membrane-bound hydrogenase (MBH) and quinone-reducing complex I are homologous respiratory complexes with a common ancestor, but a structural basis for their evolutionary ...Hydrogen gas-evolving membrane-bound hydrogenase (MBH) and quinone-reducing complex I are homologous respiratory complexes with a common ancestor, but a structural basis for their evolutionary relationship is lacking. Here, we report the cryo-EM structure of a 14-subunit MBH from the hyperthermophile Pyrococcus furiosus. MBH contains a membrane-anchored hydrogenase module that is highly similar structurally to the quinone-binding Q-module of complex I while its membrane-embedded ion-translocation module can be divided into a H- and a Na-translocating unit. The H-translocating unit is rotated 180° in-membrane with respect to its counterpart in complex I, leading to distinctive architectures for the two respiratory systems despite their largely conserved proton-pumping mechanisms. The Na-translocating unit, absent in complex I, resembles that found in the Mrp H/Na antiporter and enables hydrogen gas evolution by MBH to establish a Na gradient for ATP synthesis near 100°C. MBH also provides insights into Mrp structure and evolution of MBH-based respiratory enzymes. | |||||||||
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_7468.map.gz | 78.5 MB | EMDB map data format | |
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Header (meta data) | emd-7468-v30.xml emd-7468.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7468_fsc.xml | 9.6 KB | Display | FSC data file |
Images | emd_7468.png | 37.5 KB | ||
Filedesc metadata | emd-7468.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7468 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7468 | HTTPS FTP |
-Related structure data
Related structure data | 6cfwMC 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_7468.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryoEM structure of a respiratory membrane-bound hydrogenase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.088 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 : Membrane-bound Hydrogenase (MBH) complex
+Supramolecule #1: Membrane-bound Hydrogenase (MBH) complex
+Macromolecule #1: Monovalent cation/H+ antiporter subunit D
+Macromolecule #2: Monovalent cation/H+ antiporter subunit C
+Macromolecule #3: MBH subunit
+Macromolecule #4: MBH subunit
+Macromolecule #5: Mbh13 NADH dehydrogenase subunit
+Macromolecule #6: Monovalent cation/H+ antiporter subunit B
+Macromolecule #7: Monovalent cation/H+ antiporter subunit E
+Macromolecule #8: MBH subunit
+Macromolecule #9: Monovalent cation/H+ antiporter subunit G
+Macromolecule #10: Monovalent cation/H+ antiporter subunit F
+Macromolecule #11: Probable membrane-bound hydrogenase subunit mbhJ
+Macromolecule #12: Membrane-bound hydrogenase subunit beta
+Macromolecule #13: Membrane-bound hydrogenase subunit alpha
+Macromolecule #14: NADH-plastoquinone oxidoreductase subunit
+Macromolecule #15: IRON/SULFUR CLUSTER
+Macromolecule #16: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |