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- EMDB-4618: Cryo-EM structure of dimeric quinol dependent nitric oxide reduct... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4618 | |||||||||||||||
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Title | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans | |||||||||||||||
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![]() | Proton Transfer / Membrane Protein / Homodimer / OXIDOREDUCTASE | |||||||||||||||
Function / homology | ![]() nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / cytochrome-c oxidase activity / aerobic respiration / heme binding / membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||
![]() | Gopalasingam CC / Johnson RM / Chiduza GN | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.9 KB | Display | ![]() |
Images | ![]() | 33.2 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qq5MC ![]() 4619C ![]() 6qq6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Quinol Dependent Nitric Oxide Reductase
Entire | Name: Quinol Dependent Nitric Oxide Reductase |
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Components |
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-Supramolecule #1: Quinol Dependent Nitric Oxide Reductase
Supramolecule | Name: Quinol Dependent Nitric Oxide Reductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 170 KDa |
-Macromolecule #1: Nitric oxide reductase subunit B
Macromolecule | Name: Nitric oxide reductase subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitric oxide reductase (cytochrome c) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 83.121984 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGPYRRLWFT LIAVLAVTFA LLGFYGGEVY RQAPPIPEEV ASADGTRLFG RDDILDGQTA WQSIGGMQLG SIWGHGAYQA PDWTADWLH RELMAWLDLA ARDAHGRDYG QLDAPAQAAL REQLKAEYRA NRADAAGGKL TLSPRRAQAV AQTEAYYDQL F SDAPALHR ...String: MGPYRRLWFT LIAVLAVTFA LLGFYGGEVY RQAPPIPEEV ASADGTRLFG RDDILDGQTA WQSIGGMQLG SIWGHGAYQA PDWTADWLH RELMAWLDLA ARDAHGRDYG QLDAPAQAAL REQLKAEYRA NRADAAGGKL TLSPRRAQAV AQTEAYYDQL F SDAPALHR SRENYAMKEN TLPDANRRRQ MTHFFFWTAW AAGTEREGTS VTYTNNWPHE PLIGNHPSSE NVMWSIISVV VL LAGIGLL IWAWAFLRGK EEDEPPAPAR DPLTTFALTP SQRALGKYLF LVVALFGFQV LLGGFTAHYT VEGQKFYGID LSQ WFPYSL VRTWHIQSAL FWIATGFLAA GLFLAPLING GRDPKYQKAG VDILFWALVL VVVGSFAGNY LAIAQIMPPD LNFW LGHQG YEYVDLGRLW QIGKFAGICF WLVLMLRGIV PALRTPGGDK NLLALLTASV GAIGLFYGAG FFYGERTHLT VMEYW RWWI VHLWVEGFFE VFATTALAFI FSTLGLVSRR MATTASLASA SLFMLGGIPG TFHHLYFAGT TTPVMAVGAS FSALEV VPL IVLGHEAWEN WRLKTRAPWM ENLKWPLMCF VAVAFWNMLG AGVFGFMINP PVSLYYIQGL NTTPVHAHAA LFGVYGF LA LGFTLLVLRY IRPQYALSPG LMKLAFWGLN LGLALMIFTS LLPIGLIQFH ASVSEGMWYA RSEAFMQQDI LKTLRWGR T FGDVVFLLGA LAMVVQVILG LLSGK UniProtKB: Nitric oxide reductase subunit B |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ![]() ChemComp-HEM: |
-Macromolecule #3: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Blot for 6 seconds with blot force of 6 prior to plunge freezing. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3213 / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |