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Open data
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Basic information
Entry | Database: PDB / ID: 7awt | |||||||||
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Title | E. coli NADH quinone oxidoreductase hydrophilic arm | |||||||||
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![]() | ELECTRON TRANSPORT / E. coli / respiratory complex I | |||||||||
Function / homology | ![]() NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex I / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / metabolic process / ATP synthesis coupled electron transport ...NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex I / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / metabolic process / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||
![]() | Schimpf, J. / Grishkovskaya, I. / Haselbach, D. / Friedrich, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the peripheral arm of a minimalistic respiratory complex I. Authors: Johannes Schimpf / Sabrina Oppermann / Tatjana Gerasimova / Ana Filipa Santos Seica / Petra Hellwig / Irina Grishkovskaya / Daniel Wohlwend / David Haselbach / Thorsten Friedrich / ![]() ![]() ![]() Abstract: Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with ...Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase. Here, we report the structure of the peripheral arm of the E. coli complex I consisting of six subunits, the FMN cofactor, and nine iron-sulfur clusters at 2.7 Å resolution obtained by cryo electron microscopy. While the cofactors are in equivalent positions as in the complex from other species, individual subunits are adapted to the absence of supernumerary proteins to guarantee structural stability. The catalytically important subunits NuoC and D are fused resulting in a specific architecture of functional importance. Striking features of the E. coli complex are scrutinized by mutagenesis and biochemical characterization of the variants. Moreover, the arrangement of the subunits sheds light on the unknown assembly of the complex. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 442.8 KB | Display | ![]() |
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PDB format | ![]() | 350.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 68.8 KB | Display | |
Data in CIF | ![]() | 106.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11930MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
-NADH-quinone oxidoreductase subunit ... , 5 types, 5 molecules BDEFI
#1: Protein | Mass: 25081.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A4P6IQ32, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#2: Protein | Mass: 68321.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nuoD, nuoC, nuoCD, A9R57_03750, ACU57_26515, AUQ13_04755, BHS87_13060, BJJ90_07840, EL75_1346, EL79_1355, EL80_1377, PGD_00936 Production host: ![]() ![]() References: UniProt: A0A024L1E0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#3: Protein | Mass: 18614.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 49352.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nuoF, A6V01_13755, ACU57_26505, AMK83_13840, AML07_04350, AUQ13_04765, AUS26_02240, AW106_12795, AWB10_08250, AZZ83_002438, B7C53_18940, B9T59_22345, BANRA_00851, BANRA_03072, BANRA_04773, ...Gene: nuoF, A6V01_13755, ACU57_26505, AMK83_13840, AML07_04350, AUQ13_04765, AUS26_02240, AW106_12795, AWB10_08250, AZZ83_002438, B7C53_18940, B9T59_22345, BANRA_00851, BANRA_03072, BANRA_04773, BEN53_14595, BHF03_03880, BHF46_01730, BHS81_14175, BK248_00860, BK292_05290, BK296_01020, BK383_00250, BMA87_02945, BMT91_07775, BON65_13640, BON86_24430, BON92_12680, BON95_09120, BUE81_22605, BvCms2454_00746, BvCms28BK_03198, BvCmsHHP001_03303, BvCmsKSP026_02101, BvCmsNSP006_01096, BW690_09740, BXT93_03430, BZL31_15150, C4M78_17025, C5715_07070, C5F72_08640, C5F73_19840, C5N07_04185, C5P44_06790, C9306_02040, C9Z28_02725, C9Z39_01460, C9Z69_00815, C9Z89_04315, CDL37_03605, CI641_004330, CI693_06855, CIG45_06055, COD30_04005, CQP61_09520, CRD98_00870, D2185_05400, D3821_01640, D4628_04120, D4636_00545, D4638_01305, D4718_06850, D4V08_02555, D5H35_06205, D6004_05690, D6T98_01170, D6X36_03890, D7Z75_03825, D9610_02990, D9D44_01275, D9E49_01010, D9E73_00855, D9G11_07710, D9G69_03910, D9H10_04150, D9H53_15420, D9H70_02345, D9I18_14220, D9I87_13725, D9J03_10045, D9J11_03345, D9J52_03020, D9S45_09510, DAH32_13110, DEO04_00250, DIV22_21085, DJ492_03390, DJ503_11040, DL257_04580, DL326_06740, DL530_07780, DL705_09630, DL800_17430, DLU50_00840, DLW60_04875, DM129_02235, DM155_04030, DM267_09550, DM820_00550, DN660_04080, DN700_00545, DND79_04995, DNW42_02440, DNX30_06170, DOY67_08465, DQF71_03220, DQO13_04220, DQP61_00840, DRW19_09495, DS143_05695, DT034_07530, DTL43_00370, DTL90_13100, DTZ20_01245, DVB38_04835, DWB25_08295, E0K84_03605, E2112_03890, E2114_09530, E2115_04905, E2119_16160, E2127_14390, E2128_10460, E2129_15075, E2135_02805, E2855_02915, E2863_02877, E4K61_01395, E5S42_01460, E5S61_00535, E5S62_17345, EA184_09115, EAI52_04445, EAM59_07165, EAN70_08340, EAX79_05190, EB525_RS07480, EBM08_06425, EC1094V2_1394, EC3234A_175c00630, EC95NR1_01387, ECTO6_01644, ED178_07115, ED307_03840, ED600_10345, EEP23_07145, EG599_02320, EG796_14640, EH412_08495, EHD79_00530, EHJ36_09560, EI021_18270, EI028_02610, EI041_16810, EIA21_10570, EIZ93_06525, EKI52_23705, EL75_1348, EL79_1357, EL80_1379, ELT20_15430, ELT22_11130, ELT23_05195, ELT49_05605, ELT58_04715, ELV05_03045, ELV08_10065, EPS91_10180, EPT01_05120, EPU41_13385, ERS085379_00188, ERS085386_00208, ERS150876_02659, ExPECSC019_02995, ExPECSC038_02313, EXX06_13115, EXX24_00205, EXX55_12575, EXX71_01510, EXX87_07270, EYD11_07465, EYY27_07830, F1E13_01775, F1E19_11420, F7F00_07635, F7F18_03770, F7F23_12415, F7F26_06575, F7F29_01405, F7F56_01340, F9059_05310, F9225_15495, F9Z74_15180, FORC82_1552, FQ022_16920, FQ915_15315, FV293_06770, FV295_04395, FWK02_17585, FZ043_16850, FZN06_04430, G3V64_01355, G5616_08820, G5668_05175, G5670_05315, G5680_07940, GHR40_12060, GII67_01480, GII91_07865, GIJ01_18890, GKF21_10745, GKF28_09910, GKF34_10195, GKF39_02500, GKF47_10255, GKF52_10320, GKF74_02415, GKF86_02460, GKF89_15750, GKG08_04525, GKG09_03430, GKG11_03430, GKG12_06425, GKG22_03430, GKG29_03430, GP654_10525, GP662_01335, GP664_02125, GP666_01245, GP678_01495, GP689_04555, GP700_00840, GP727_18600, GP892_00660, GP912_01620, GP935_11155, GQA23_00845, GQE30_00240, GQE34_00275, GQE51_04055, GQE64_02710, GQM17_00600, GQM18_11425, GRW05_01905, GRW12_05105, GRW27_13850, GRW42_12615, GRW81_01585, HmCmsJML079_03904, NCTC10082_04010, NCTC10766_00211, NCTC12650_01901, NCTC13846_01677, NCTC7927_01818, NCTC8450_03934, NCTC8500_01767, NCTC8622_03891, NCTC8960_04372, NCTC9007_03395, NCTC9045_01880, NCTC9062_01542, NCTC9111_05438, NCTC9117_02186, NCTC9119_01758, NCTC9703_00796, NCTC9706_04854, NCTC9777_05069, NCTC9962_07097, NCTC9969_01783, PGD_00938, RK56_005495, SAMEA3472047_02540, SAMEA3472055_03856, SAMEA3472056_00576, SAMEA3472110_03603, SAMEA3472112_03618, SAMEA3472147_01543, SAMEA3484427_04453, SAMEA3484429_04478, SAMEA3485101_03070, SAMEA3752372_03727, SAMEA3752557_00624, SAMEA3752559_01734, SAMEA3753300_00090, UN86_09935 Production host: ![]() ![]() References: UniProt: A0A037YNA7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#6: Protein | Mass: 20562.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein , 1 types, 1 molecules G
#5: Protein | Mass: 100419.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nuoG, ACU57_26500, AUQ13_04770, BMA87_02940, BON75_03580, BON98_08405, BUE81_22600, BvCms2454_00747, BvCmsHHP001_03304, BvCmsHHP019_02167, BvCmsKSP026_02100, BvCmsSINP011_02783, BZL31_15145, ...Gene: nuoG, ACU57_26500, AUQ13_04770, BMA87_02940, BON75_03580, BON98_08405, BUE81_22600, BvCms2454_00747, BvCmsHHP001_03304, BvCmsHHP019_02167, BvCmsKSP026_02100, BvCmsSINP011_02783, BZL31_15145, C5F72_08645, C5F73_19835, C5N07_04190, C9Z39_01455, CG692_14695, CI693_06850, CIG45_06060, D2185_05395, D3821_01645, D4638_01300, D4718_06845, DJ503_11035, DL326_06735, DT034_07525, DTL43_00365, E2119_16155, E2134_04090, E2135_02800, E4K61_01390, EAI52_04450, ECTO6_01645, EI021_18275, EI028_02615, EI041_16815, EIZ93_06530, ELT20_15435, EPT01_05125, EXX71_01505, EYD11_07470, F1E19_11415, FV293_06765, GHR40_12065, GKF39_02495, GKF74_02420, GKF86_02455, GKF89_15755, GP671_02435, GP689_04560, GQE33_01795, GQE34_00280, GQM17_00605, GRW05_01910, GRW27_13855, GRW80_02440, GRW81_01580, NCTC10963_01653, NCTC11022_02277, NCTC12650_01902, NCTC9045_01881, NCTC9062_01541, NCTC9117_02187, PGD_00939, RK56_005500, SAMEA3472047_02539, SAMEA3484427_04454, SAMEA3484429_04477, SAMEA3752559_01733, SAMEA3753300_00091 Production host: ![]() ![]() References: UniProt: A0A037YPU0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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-Non-polymers , 5 types, 143 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-SF4 / #8: Chemical | #9: Chemical | ChemComp-MG / #10: Chemical | ChemComp-FMN / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: NADH quinone oxidoreductase hydrophilic arm / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 6 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 67 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
Software | Name: PHENIX / Version: 1.17_3644: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223751 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4HEA Accession code: 4HEA / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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