7AWT

E. coli NADH quinone oxidoreductase hydrophilic arm


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the peripheral arm of a minimalistic respiratory complex I.

Schimpf, J.Oppermann, S.Gerasimova, T.Santos Seica, A.F.Hellwig, P.Grishkovskaya, I.Wohlwend, D.Haselbach, D.Friedrich, T.

(2022) Structure 30: 80

  • DOI: 10.1016/j.str.2021.09.005
  • Primary Citation of Related Structures:  
    7AWT

  • PubMed 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 neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase ...

    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.


    Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany. Electronic address: friedrich@bio.chemie.uni-freiburg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BA [auth B]220Escherichia coliMutation(s): 0 
Gene Names: nuoBEJC75_10485
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFC7 (Escherichia coli (strain K12))
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UniProt GroupP0AFC7
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/DB [auth D]596Escherichia coliMutation(s): 0 
Gene Names: 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P33599 (Escherichia coli (strain K12))
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UniProt GroupP33599
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit EC [auth E]166Escherichia coliMutation(s): 0 
EC: 7.1.1
UniProt
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UniProt GroupP0AFD1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FD [auth F]445Escherichia coliMutation(s): 0 
Gene Names: 
nuoFA6V01_13755ACU57_26505AMK83_13840AML07_04350AUQ13_04765AUS26_02240AW106_12795AWB10_08250AZZ83_002438B7C53_18940B9T59_22345BANRA_00851BANRA_03072BANRA_04773BEN53_14595BHF03_03880BHF46_01730BHS81_14175BK248_00860BK292_05290BK296_01020BK383_00250BMA87_02945BMT91_07775BON65_13640BON86_24430BON92_12680BON95_09120BUE81_22605BvCms2454_00746BvCms28BK_03198BvCmsHHP001_03303BvCmsKSP026_02101BvCmsNSP006_01096BW690_09740BXT93_03430BZL31_15150C4M78_17025C5715_07070C5F72_08640C5F73_19840C5N07_04185C5P44_06790C9306_02040C9Z28_02725C9Z39_01460C9Z69_00815C9Z89_04315CDL37_03605CI641_004330CI693_06855CIG45_06055COD30_04005CQP61_09520CRD98_00870D2185_05400D3821_01640D4628_04120D4636_00545D4638_01305D4718_06850D4V08_02555D5H35_06205D6004_05690D6T98_01170D6X36_03890D7Z75_03825D9610_02990D9D44_01275D9E49_01010D9E73_00855D9G11_07710D9G69_03910D9H10_04150D9H53_15420D9H70_02345D9I18_14220D9I87_13725D9J03_10045D9J11_03345D9J52_03020D9S45_09510DAH32_13110DEO04_00250DIV22_21085DJ492_03390DJ503_11040DL257_04580DL326_06740DL530_07780DL705_09630DL800_17430DLU50_00840DLW60_04875DM129_02235DM155_04030DM267_09550DM820_00550DN660_04080DN700_00545DND79_04995DNW42_02440DNX30_06170DOY67_08465DQF71_03220DQO13_04220DQP61_00840DRW19_09495DS143_05695DT034_07530DTL43_00370DTL90_13100DTZ20_01245DVB38_04835DWB25_08295E0K84_03605E2112_03890E2114_09530E2115_04905E2119_16160E2127_14390E2128_10460E2129_15075E2135_02805E2855_02915E2863_02877E4K61_01395E5S42_01460E5S61_00535E5S62_17345EA184_09115EAI52_04445EAM59_07165EAN70_08340EAX79_05190EB525_RS07480EBM08_06425EC1094V2_1394EC3234A_175c00630EC95NR1_01387ECTO6_01644ED178_07115ED307_03840ED600_10345EEP23_07145EG599_02320EG796_14640EH412_08495EHD79_00530EHJ36_09560EI021_18270EI028_02610EI041_16810EIA21_10570EIZ93_06525EKI52_23705EL75_1348EL79_1357EL80_1379ELT20_15430ELT22_11130ELT23_05195ELT49_05605ELT58_04715ELV05_03045ELV08_10065EPS91_10180EPT01_05120EPU41_13385ERS085379_00188ERS085386_00208ERS150876_02659ExPECSC019_02995ExPECSC038_02313EXX06_13115EXX24_00205EXX55_12575EXX71_01510EXX87_07270EYD11_07465EYY27_07830F1E13_01775F1E19_11420F7F00_07635F7F18_03770F7F23_12415F7F26_06575F7F29_01405F7F56_01340F9059_05310F9225_15495F9Z74_15180FORC82_1552FQ022_16920FQ915_15315FV293_06770FV295_04395FWK02_17585FZ043_16850FZN06_04430G3V64_01355G5616_08820G5668_05175G5670_05315G5680_07940GHR40_12060GII67_01480GII91_07865GIJ01_18890GKF21_10745GKF28_09910GKF34_10195GKF39_02500GKF47_10255GKF52_10320GKF74_02415GKF86_02460GKF89_15750GKG08_04525GKG09_03430GKG11_03430GKG12_06425GKG22_03430GKG29_03430GP654_10525GP662_01335GP664_02125GP666_01245GP678_01495GP689_04555GP700_00840GP727_18600GP892_00660GP912_01620GP935_11155GQA23_00845GQE30_00240GQE34_00275GQE51_04055GQE64_02710GQM17_00600GQM18_11425GRW05_01905GRW12_05105GRW27_13850GRW42_12615GRW81_01585HmCmsJML079_03904NCTC10082_04010NCTC10766_00211NCTC12650_01901NCTC13846_01677NCTC7927_01818NCTC8450_03934NCTC8500_01767NCTC8622_03891NCTC8960_04372NCTC9007_03395NCTC9045_01880NCTC9062_01542NCTC9111_05438NCTC9117_02186NCTC9119_01758NCTC9703_00796NCTC9706_04854NCTC9777_05069NCTC9962_07097NCTC9969_01783PGD_00938RK56_005495SAMEA3472047_02540SAMEA3472055_03856SAMEA3472056_00576SAMEA3472110_03603SAMEA3472112_03618SAMEA3472147_01543SAMEA3484427_04453SAMEA3484429_04478SAMEA3485101_03070SAMEA3752372_03727SAMEA3752557_00624SAMEA3752559_01734SAMEA3753300_00090UN86_09935

EC: 7.1.1
UniProt
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UniProt GroupP31979
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductaseE [auth G]908Escherichia coliMutation(s): 0 
Gene Names: 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupP33602
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IF [auth I]180Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupP0AFD6
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
K [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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G [auth B],
J [auth F],
N [auth G],
O [auth G],
P [auth G],
G [auth B],
J [auth F],
N [auth G],
O [auth G],
P [auth G],
W [auth I],
X [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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H [auth E],
M [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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I [auth E],
L [auth F],
Q [auth G],
R [auth G],
S [auth G],
I [auth E],
L [auth F],
Q [auth G],
R [auth G],
S [auth G],
T [auth G],
U [auth G],
V [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany278002225/RTG 2202
German Research Foundation (DFG)GermanySPP 1927

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2022-01-19
    Changes: Database references