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Yorodumi- PDB-6qq6: Cryo-EM structure of dimeric quinol dependent nitric oxide reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qq6 | |||||||||||||||
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Title | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) Val495Ala mutant from Alcaligenes xylosoxidans | |||||||||||||||
Components | Nitric oxide reductase subunit B | |||||||||||||||
Keywords | OXIDOREDUCTASE / Proton Transfer / Membrane Protein / Homodimer | |||||||||||||||
Function / homology | Function and homology information nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / cytochrome-c oxidase activity / aerobic respiration / heme binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Alcaligenes xylosoxydans xylosoxydans (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Gopalasingam, C.C. / Johnson, R.M. / Chiduza, G.N. / Tosha, T. / Yamamoto, M. / Shiro, Y. / Antonyuk, S.V. / Muench, S.P. / Hasnain, S.S. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Sci Adv / Year: 2019 Title: Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy. Authors: Chai C Gopalasingam / Rachel M Johnson / George N Chiduza / Takehiko Tosha / Masaki Yamamoto / Yoshitsugu Shiro / Svetlana V Antonyuk / Stephen P Muench / S Samar Hasnain / Abstract: Quinol-dependent nitric oxide reductases (qNORs) are membrane-integrated, iron-containing enzymes of the denitrification pathway, which catalyze the reduction of nitric oxide (NO) to the major ozone ...Quinol-dependent nitric oxide reductases (qNORs) are membrane-integrated, iron-containing enzymes of the denitrification pathway, which catalyze the reduction of nitric oxide (NO) to the major ozone destroying gas nitrous oxide (NO). Cryo-electron microscopy structures of active qNOR from and an activity-enhancing mutant have been determined to be at local resolutions of 3.7 and 3.2 Å, respectively. They unexpectedly reveal a dimeric conformation (also confirmed for qNOR from ) and define the active-site configuration, with a clear water channel from the cytoplasm. Structure-based mutagenesis has identified key residues involved in proton transport and substrate delivery to the active site of qNORs. The proton supply direction differs from cytochrome c-dependent NOR (cNOR), where water molecules from the cytoplasm serve as a proton source similar to those from cytochrome c oxidase. | |||||||||||||||
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 | 6qq6.cif.gz | 276.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qq6.ent.gz | 221.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qq6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6qq6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6qq6_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 6qq6_validation.cif.gz | 73.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qq6 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qq6 | HTTPS FTP |
-Related structure data
Related structure data | 4619MC 4618C 6qq5C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 83093.938 Da / Num. of mol.: 2 / Mutation: V495A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria) Gene: norB_1, ERS451415_02175 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: A0A0D6H8R3, nitric oxide reductase (cytochrome c) #6: Sugar | |
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-Non-polymers , 5 types, 29 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | #4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | |
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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: Quinol Dependent Nitric Oxide Reductase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.17 MDa / Experimental value: NO |
Source (natural) | Organism: Achromobacter xylosoxidans (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41 (DE3) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Blot for 6 seconds with blot force of 6 prior to plunge freezing |
-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 magnification: 47710 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1803 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 614931 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227359 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6QQ5 Accession code: 6QQ5 / Source name: PDB / Type: experimental model |