+Open data
-Basic information
Entry | Database: PDB / ID: 6cfw | ||||||
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Title | cryoEM structure of a respiratory membrane-bound hydrogenase | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / respiratory / hydrogenase / ion translocation | ||||||
Function / homology | Function and homology information : / ferredoxin hydrogenase / monoatomic ion transmembrane transporter activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / proton motive force-driven ATP synthesis / nickel cation binding / quinone binding ...: / ferredoxin hydrogenase / monoatomic ion transmembrane transporter activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / proton motive force-driven ATP synthesis / nickel cation binding / quinone binding / NADH dehydrogenase (ubiquinone) activity / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus COM1 (archaea) Pyrococcus furiosus (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Li, H.L. / Yu, H.J. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6cfw.cif.gz | 441.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cfw.ent.gz | 355.2 KB | Display | PDB format |
PDBx/mmJSON format | 6cfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cfw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6cfw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6cfw_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 6cfw_validation.cif.gz | 110.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cfw ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cfw | HTTPS FTP |
-Related structure data
Related structure data | 7468MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Monovalent cation/H+ antiporter subunit ... , 6 types, 6 molecules HGFACB
#1: Protein | Mass: 55016.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06375 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UQL5 |
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#2: Protein | Mass: 12784.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06370 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UZU1 |
#6: Protein | Mass: 15531.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06365 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6TXN5 |
#7: Protein | Mass: 18750.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06340 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6TXN1 |
#9: Protein | Mass: 13521.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06350 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UQL1 |
#10: Protein | Mass: 9063.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06345 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UZT7 |
-Protein , 6 types, 6 molecules DIMEJN
#3: Protein | Mass: 10423.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1426 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U104 |
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#4: Protein | Mass: 13055.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06380 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6U847 |
#5: Protein | Mass: 35414.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06400 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6UQM0 |
#8: Protein | Mass: 11149.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06360 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6V287 |
#11: Protein | Mass: 18324.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mbhJ, mbh10, PF1432 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U0Z8, ferredoxin hydrogenase |
#14: Protein | Mass: 15707.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_06405 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: I6U851 |
-Membrane-bound hydrogenase subunit ... , 2 types, 2 molecules KL
#12: Protein | Mass: 20213.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mbhK, mbh11, PF1433 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U0Z7, ferredoxin hydrogenase |
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#13: Protein | Mass: 43008.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: mbhL, mbh12, PF1434 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: Q8U0Z6, ferredoxin hydrogenase |
-Non-polymers , 2 types, 4 molecules
#15: Chemical | #16: Chemical | ChemComp-NFU / | |
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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: Membrane-bound Hydrogenase (MBH) complex / Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
Source (recombinant) | Organism: Pyrococcus furiosus (archaea) |
Buffer solution | pH: 8.2 |
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 |
Image recording | Electron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131679 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.7 Å | ||||||||||||||||||||||||
Refine LS restraints |
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