|Entry||Database: EMDB / ID: EMD-4618|
|Title||Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans|
|Sample||Quinol Dependent Nitric Oxide Reductase:|
Nitric oxide reductase subunit B / (ligand) x 3
|Function / homology|
Function and homology information
nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / cytochrome-c oxidase activity / aerobic respiration / heme binding / integral component of membrane
Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I
Nitric oxide reductase subunit B
|Biological species||Achromobacter xylosoxidans (bacteria) / Alcaligenes xylosoxydans xylosoxydans (bacteria)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.9 Å|
|Authors||Gopalasingam CC / Johnson RM / Chiduza GN / Tosha T / Yamamoto M / Shiro Y / Antonyuk SV / Muench SP / Hasnain SS|
|Funding support|| United Kingdom, 4 items |
|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.
|Validation Report||PDB-ID: 6qq5|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_4618.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.07 Å|
|Symmetry||Space group: 1|
CCP4 map header:
+Entire Quinol Dependent Nitric Oxide Reductase
|Entire||Name: Quinol Dependent Nitric Oxide Reductase / Number of components: 5|
+Component #1: protein, Quinol Dependent Nitric Oxide Reductase
|Protein||Name: Quinol Dependent Nitric Oxide Reductase / Recombinant expression: No|
|Mass||Theoretical: 170 kDa|
|Source||Species: Achromobacter xylosoxidans (bacteria)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria) / Strain: C41 (DE3)|
+Component #2: protein, Nitric oxide reductase subunit B
|Protein||Name: Nitric oxide reductase subunit B / Number of Copies: 2 / Recombinant expression: No|
|Mass||Theoretical: 83.121984 kDa|
|Source||Species: Alcaligenes xylosoxydans xylosoxydans (bacteria)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria)|
+Component #3: ligand, PROTOPORPHYRIN IX CONTAINING FE
|Ligand||Name: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 0.616487 kDa|
+Component #4: ligand, FE (III) ION
|Ligand||Name: FE (III) ION / Number of Copies: 2 / Recombinant expression: No|
|Mass||Theoretical: 5.584505 MDa|
+Component #5: ligand, CALCIUM ION
|Ligand||Name: CALCIUM IONCalcium / Number of Copies: 2 / Recombinant expression: No|
|Mass||Theoretical: 4.007805 MDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 3 mg/mL / pH: 7|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
Details: Blot for 6 seconds with blot force of 6 prior to plunge freezing.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 65 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500.0 - -3500.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 3213|
-Atomic model buiding
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