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- PDB-8qhk: Crystal structure of reduced respiratory Complex I subunits NuoEF... -

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Basic information

Entry
Database: PDB / ID: 8qhk
TitleCrystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 3-acetylpyridine adenine dinucleotide
Components(NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 2
KeywordsOXIDOREDUCTASE / Complex I / respiratory chain / 3-acetylpyridine adenine dinucleotide / ligand complex
Function / homology
Function and homology information


plasma membrane respiratory chain complex I / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ...Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like superfamily
Similarity search - Domain/homology
ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED / FE2/S2 (INORGANIC) CLUSTER / Chem-FNR / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsWohlwend, D. / Friedrich, T. / Bucka, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I.
Authors: Wohlwend, D. / Merono, L. / Bucka, S. / Ritter, K. / Jessen, H.J. / Friedrich, T.
History
DepositionSep 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,48124
Polymers134,1944
Non-polymers4,28720
Water16,790932
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-119 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.413, 116.013, 189.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD

#1: Protein NADH-quinone oxidoreductase subunit E / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit E / NDH-1 subunit E


Mass: 18573.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-28b(+)::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase (quinone)


Mass: 48523.301 Da / Num. of mol.: 2 / Mutation: 427AGHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O66841

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Non-polymers , 8 types, 952 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-AP0 / ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED


Mass: 664.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 932 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: Tris, BisTris, trisodium citrate, ammonium sulfate, NaCl
PH range: 6.3 - 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.538 Å / Num. obs: 102689 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 15.7
Reflection shellResolution: 1.95→1.98 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5013 / CC1/2: 0.737 / Rpim(I) all: 0.436

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimless0.7.9data scaling
REFMAC5.8.0352phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→49.538 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.142 / SU B: 7.742 / SU ML: 0.108 / Average fsc free: 0.9658 / Average fsc work: 0.9742 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2003 5309 5.174 %
Rwork0.1666 97303 -
all0.168 --
obs-102612 99.787 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.298 Å20 Å2-0 Å2
2--1.723 Å20 Å2
3----1.425 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9069 0 231 932 10232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129684
X-RAY DIFFRACTIONr_bond_other_d0.0040.0168814
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.6513150
X-RAY DIFFRACTIONr_angle_other_deg0.4011.57320602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26751170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.687551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.388101623
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.23109
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.43610427
X-RAY DIFFRACTIONr_chiral_restr0.0590.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021881
X-RAY DIFFRACTIONr_nbd_refined0.2040.21989
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.28468
X-RAY DIFFRACTIONr_nbtor_refined0.180.24711
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2806
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0940.22
X-RAY DIFFRACTIONr_metal_ion_refined0.10.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.30.224
X-RAY DIFFRACTIONr_nbd_other0.2080.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.227
X-RAY DIFFRACTIONr_mcbond_it0.7521.7374653
X-RAY DIFFRACTIONr_mcbond_other0.7511.7374653
X-RAY DIFFRACTIONr_mcangle_it1.2182.65832
X-RAY DIFFRACTIONr_mcangle_other1.2172.6015833
X-RAY DIFFRACTIONr_scbond_it1.1041.9195031
X-RAY DIFFRACTIONr_scbond_other1.0251.8965012
X-RAY DIFFRACTIONr_scangle_it1.7472.8267290
X-RAY DIFFRACTIONr_scangle_other1.6422.797261
X-RAY DIFFRACTIONr_lrange_it5.9527.86511249
X-RAY DIFFRACTIONr_lrange_other5.81725.30110993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.2893890.28370960.28375280.9330.93699.42880.249
2.001-2.0550.2773780.26568800.26672840.9430.94499.64310.229
2.055-2.1150.2523800.23967380.23971460.9480.95699.60820.2
2.115-2.180.2463610.21265240.21469100.9560.96899.63820.176
2.18-2.2510.2283460.19363270.19566880.9640.97399.77570.157
2.251-2.330.2173550.18261270.18464980.9680.97899.75380.147
2.33-2.4180.2193250.18259530.18462870.9680.97899.85680.148
2.418-2.5160.2043080.16957240.1760400.9740.98299.86760.137
2.516-2.6280.193140.16255100.16458280.9770.98499.93140.133
2.628-2.7560.2092870.16253020.16455920.9730.98499.94640.136
2.756-2.9040.2232670.15349950.15752630.9730.98699.9810.13
2.904-3.080.2112590.16547740.16750340.9710.98399.98010.141
3.08-3.2910.1982670.16244580.16447250.9740.9841000.144
3.291-3.5540.1912260.15842060.1644330.9770.98699.97740.144
3.554-3.8910.1791880.14339080.14540960.9820.9891000.133
3.891-4.3470.1481740.12435280.12537030.9860.99199.9730.118
4.347-5.0130.1741680.12731480.1333160.9860.9911000.123
5.013-6.1240.1961520.15226850.15528370.9770.9881000.144
6.124-8.5950.1731100.15121270.15222370.9860.9871000.146
8.595-49.5380.145550.17512930.17413480.9860.9811000.172
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1237-0.86350.49091.0411-0.07012.12710.23220.2969-0.453-0.1457-0.0170.19150.71820.1322-0.21520.39760.0253-0.1080.0676-0.04470.145327.3776-10.5507-60.0205
21.7240.04870.19590.5811-0.25412.16050.03850.1540.0931-0.02990.0212-0.015-0.05150.083-0.05970.0997-0.0173-0.01120.02320.02120.066825.831512.7697-54.3834
33.13660.804-0.42490.87110.02791.73190.1905-0.50610.6910.103-0.0850.1746-0.59990.1665-0.10550.3535-0.05320.04490.1384-0.0890.2231-3.92411.0549-12.2916
42.10170.04230.29780.4809-0.16932.03440.0748-0.1485-0.13870.0269-0.033-0.02920.13730.2144-0.04190.11330.0193-0.00330.03990.01290.079-5.6122-11.881-18.4626
Refinement TLS groupSelection: ALL

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