Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit A
Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit B
Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit C
Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit D
Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit E
Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit F
Ligand: FLAVIN MONONUCLEOTIDE
Ligand: RIBOFLAVIN
Ligand: UBIQUINONE-1
Ligand: FE2/S2 (INORGANIC) CLUSTER
Function / homology
Function and homology information
NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI151152
United States
Citation
Journal: To Be Published Title: Novel cofactor binding motifs, electron transfer and ion pumping mechanisms of the respiratory complex NQR Authors: Juarez O / Fuller JR
Map sharpened by fitted Bfactor (-29.6032) and filtered to local resolution via the Relion LocalRes method. Model was built and refined primarily into this map, including model ADPs.
Details: 100 mM KCl, 1 mM EDTA, 50 mM HEPES, pH 7.0
Grid
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: Gatan Solarus plasma cleaner operated at 20W and using ambient/room air
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: A 3.5 uL droplet of sample was applied to the grid surface and blotted for 4 s before plunging into liquid ethane..
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Software
Name: EPU (ver. 2.9)
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3159 / Average exposure time: 4.66 sec. / Average electron dose: 50.0 e/Å2 / Details: 50 e-/A2 fractionated over 40 movie frames
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Type of model: OTHER Details: 3D initial model generated from a subset of the data itself using RELION 4.0beta2
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65159 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0beta2) / Number images used: 73763
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0beta2)
Final 3D classification
Number classes: 2 / Avg.num./class: 90115 / Software - Name: RELION (ver. 4.0beta2) Details: A final fixed-posed 3D classification was used to separate the two conformations of the NqrE subunit
FSC plot (resolution estimation)
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Atomic model buiding 1
Software
Name: UCSF Chimera
Details
The model was refined by iterating between manual edits in Coot, molecular dynamics-guided edits using the ISOLDE ChimeraX package, and automated real-space refinement in Phenix. Models that had been automatically rebuilt using Rosetta were used as guides during manual refinement.
Refinement
Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation
Output model
PDB-8ew3: Cryo EM structure of Vibrio cholerae NQR
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