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- PDB-9fe5: Crystal Structure of NuoEF variant R66G(NuoF) from Aquifex aeolic... -

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Basic information

Entry
Database: PDB / ID: 9fe5
TitleCrystal Structure of NuoEF variant R66G(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions after 10 min soaking
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsELECTRON TRANSPORT / Complex I / respiratory chain / NADH-ubiquinone oxidoreductase / bioenergetics
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (ubiquinone) activity / quinone binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / 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 / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain ...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 / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Chem-FNR / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 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: 2.1 Å
AuthorsWohlwend, D. / Friedrich, T. / Goeppert-Asadollahpour, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2202; 235777276/RTG Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I).
Authors: Goppert-Asadollahpour, S. / Wohlwend, D. / Friedrich, T.
History
DepositionMay 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)138,45030
Polymers133,9944
Non-polymers4,45626
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, NuoEF forms a stable (NuoEF)2 heterotetramer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18050 Å2
ΔGint-319 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.184, 116.158, 189.651
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 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 (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit F


Mass: 48423.160 Da / Num. of mol.: 2 / Mutation: R66G
Source method: isolated from a genetically manipulated source
Details: The sequence AGHHHHHH is a C-terminal affinity tag for the affinity purification of the NuoEF complex
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoEFhis / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O66841

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Non-polymers , 9 types, 804 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) 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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM BisTris pH 6.5, 1.4 M ammonium sulfate, 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.1→47.948 Å / Num. obs: 82223 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.996 / Rpim(I) all: 0.064 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4445 / CC1/2: 0.776 / Rpim(I) all: 0.476

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSVERSION Jan 31, 2020 BUILT=20200131data reduction
Aimless0.7.15data scaling
REFMAC5.8.0425phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→47.948 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.307 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.206 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4065 5.029 %Rfree flags were transferred from scaled data of previously solved structure 9FDJ
Rwork0.1803 76765 --
all0.182 ---
obs-80830 98.158 %-
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: 32.922 Å2
Baniso -1Baniso -2Baniso -3
1--0.921 Å2-0 Å20 Å2
2--1.74 Å20 Å2
3----0.818 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9105 0 236 778 10119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129652
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169018
X-RAY DIFFRACTIONr_angle_refined_deg1.21.84813124
X-RAY DIFFRACTIONr_angle_other_deg0.4231.76820870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18651162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.759549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.651101619
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg13.5471016
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.57910423
X-RAY DIFFRACTIONr_chiral_restr0.0610.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022093
X-RAY DIFFRACTIONr_nbd_refined0.210.22054
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.28678
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24693
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2720
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.22
X-RAY DIFFRACTIONr_metal_ion_refined0.170.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.213
X-RAY DIFFRACTIONr_nbd_other0.1530.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1770.22
X-RAY DIFFRACTIONr_mcbond_it0.7271.7544639
X-RAY DIFFRACTIONr_mcbond_other0.7271.7544639
X-RAY DIFFRACTIONr_mcangle_it1.2193.1495804
X-RAY DIFFRACTIONr_mcangle_other1.2193.155805
X-RAY DIFFRACTIONr_scbond_it1.0511.9435013
X-RAY DIFFRACTIONr_scbond_other0.9941.9224990
X-RAY DIFFRACTIONr_scangle_it1.7543.5227292
X-RAY DIFFRACTIONr_scangle_other1.6683.4837257
X-RAY DIFFRACTIONr_lrange_it5.20919.22311109
X-RAY DIFFRACTIONr_lrange_other5.11818.31510930
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
2.1-2.1540.3143080.25956500.26259640.9360.95399.89940.235
2.154-2.2130.2723340.24654770.24758240.9550.9699.77680.22
2.213-2.2770.5992160.51642270.5257390.4630.55377.41770.511
2.277-2.3470.2362700.20452740.20655450.9670.97399.9820.179
2.347-2.4240.2312840.19150770.19353620.9680.97899.98130.166
2.424-2.5090.2272610.18849420.1952040.9660.97999.98080.161
2.509-2.6030.2262450.17747680.1850130.9690.9811000.153
2.603-2.7090.212090.17746360.17848460.9710.98199.97940.153
2.709-2.8290.2392460.17944110.18246570.9650.9811000.16
2.829-2.9670.1932090.17142420.17244520.9760.98299.97750.154
2.967-3.1270.2162300.16840220.1742540.9740.98399.9530.154
3.127-3.3160.2281950.17338460.17640440.9690.98299.92580.162
3.316-3.5430.2041640.1636060.16237740.9780.98599.8940.151
3.543-3.8250.1891830.17132670.17235400.9790.98497.45760.16
3.825-4.1880.1631700.14230890.14332930.9830.98898.96750.137
4.188-4.6780.1771570.12228010.12529610.9840.99299.89870.123
4.678-5.3930.1871190.14525300.14726520.9820.9999.88690.146
5.393-6.5840.1881310.16221440.16322810.9820.98899.7370.162
6.584-9.2250.166840.14817180.14918060.9830.98899.77850.154
9.225-47.9480.168500.15510380.15511020.9870.98798.72960.163
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)
13.0262-0.4769-0.37190.8827-0.0631.36490.10970.40470.6719-0.0836-0.0481-0.1218-0.4129-0.0954-0.06160.34110.00790.02960.15360.05970.1586-27.286711.101812.045
21.83340.06510.6420.44320.1721.65250.097-0.021-0.11570.0261-0.03060.01550.1689-0.1308-0.06640.2045-0.0290.00750.0689-0.00160.0104-25.8247-11.962418.3947
31.9970.70350.25911.0320.08611.67050.123-0.2233-0.41640.0873-0.0051-0.17940.5392-0.0201-0.1180.40940.0082-0.05260.0660.03350.0934-58.4438-10.763960.2506
41.3357-0.0306-0.06840.43230.23491.99210.0063-0.05060.0891-0.00610.0365-0.0039-0.102-0.0284-0.04280.19910.0145-0.00170.0076-0.00310.0069-57.256612.733854.4142
Refinement TLS groupSelection: ALL

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