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- PDB-9fea: Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquif... -

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Basic information

Entry
Database: PDB / ID: 9fea
TitleCrystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NAD+
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 / NICOTINAMIDE-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 / MOLECULAR REPLACEMENT / Resolution: 1.66 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

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)138,67035
Polymers134,3144
Non-polymers4,35631
Water20,8251156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, The tetrameric assembly of two NuoEF heterodimers into a tetramer is the stable assembly in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.582, 115.785, 190.011
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_P228R / 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 / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 48583.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal sequence AGHHHHHH is an artificial affinity tag used for affinity purification of the NuoEF complex
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Plasmid: pET-28b(+)::nuoEFhis_P228R / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 9 types, 1187 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.: 5 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: 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
#9: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / 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: 52.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM BisTris pH 6.5, 1.6 M ammonium sulfate, 150 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: 1.66→49.486 Å / Num. obs: 161000 / % possible obs: 97.2 % / Redundancy: 4 % / CC1/2: 0.993 / Rpim(I) all: 0.064 / Net I/σ(I): 6.9
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 7841 / CC1/2: 0.62 / Rpim(I) all: 0.506

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSVERSION Jan 31, 2020 BUILT=20200131data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→49.486 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.17 / SU B: 3.815 / SU ML: 0.071 / Average fsc free: 0.9675 / Average fsc work: 0.9721 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 7928 4.93 %Random selection
Rwork0.1729 152870 --
all0.174 ---
obs-160798 96.865 %-
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: 22.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.196 Å20 Å2-0 Å2
2--0.732 Å20 Å2
3----0.928 Å2
Refinement stepCycle: LAST / Resolution: 1.66→49.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 211 1156 10505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129718
X-RAY DIFFRACTIONr_bond_other_d0.0020.0169110
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.84813214
X-RAY DIFFRACTIONr_angle_other_deg0.5171.76621072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03151173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.829557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.391101655
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg14.7951016
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09310436
X-RAY DIFFRACTIONr_chiral_restr0.0750.21397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022147
X-RAY DIFFRACTIONr_nbd_refined0.2240.22013
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.28656
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24744
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2908
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1880.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.217
X-RAY DIFFRACTIONr_nbd_other0.1920.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2010.21
X-RAY DIFFRACTIONr_mcbond_it0.9511.2124665
X-RAY DIFFRACTIONr_mcbond_other0.951.2124665
X-RAY DIFFRACTIONr_mcangle_it1.5792.1715847
X-RAY DIFFRACTIONr_mcangle_other1.5792.1725848
X-RAY DIFFRACTIONr_scbond_it1.6141.475053
X-RAY DIFFRACTIONr_scbond_other1.5651.4525034
X-RAY DIFFRACTIONr_scangle_it2.562.6267339
X-RAY DIFFRACTIONr_scangle_other2.4872.5937310
X-RAY DIFFRACTIONr_lrange_it6.04615.98611431
X-RAY DIFFRACTIONr_lrange_other5.87613.8611078
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
1.66-1.7030.3086060.297111200.298121780.9320.93896.28840.288
1.703-1.750.2785570.265108300.266118000.9450.95396.50.252
1.75-1.80.285700.245105220.247115000.9530.9696.45220.23
1.8-1.8560.2295010.208103370.209112290.9660.96996.51790.191
1.856-1.9160.2234800.20599750.206108390.9640.96596.45720.181
1.916-1.9840.2165060.19797250.198105280.9660.96697.1790.172
1.984-2.0580.214720.19592660.196101500.9680.96795.94090.168
2.058-2.1420.2224780.18890320.18997800.9660.97297.23930.167
2.142-2.2370.1884380.16887060.16993870.9770.97997.41130.151
2.237-2.3460.1824420.15782440.15889860.9780.98496.66150.145
2.346-2.4730.1874230.1578660.15185610.9780.98696.82280.143
2.473-2.6220.1863730.14875300.1581280.980.98697.23180.144
2.622-2.8030.1933740.15770060.15976200.9760.98596.85040.154
2.803-3.0270.1933350.15565610.15771640.9760.98596.25910.157
3.027-3.3140.1723260.15561510.15665890.9820.98798.30020.162
3.314-3.7040.1652780.15356000.15459890.9850.98898.14660.164
3.704-4.2730.1582770.13249340.13353280.9860.9997.80410.146
4.273-5.2230.1542240.14241890.14345230.990.99197.5680.163
5.223-7.3460.2291720.19933190.20135920.9770.98397.18820.221
7.346-49.4860.23960.22319580.22421230.9660.97296.74990.254
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)
15.53-5.80254.528811.6229-2.59764.6865-0.35730.2460.7121-0.0882-0.0879-0.6545-0.6480.30470.44520.3442-0.11320.06760.22930.0350.448-11.261920.730112.8211
23.1491-0.62350.81782.3157-0.35191.84330.07880.3030.5378-0.1864-0.0748-0.2784-0.32250.1802-0.0040.1412-0.05260.06380.15290.06790.1629-14.178310.457.8432
32.339-0.5416-0.23212.54610.06351.58130.0570.13460.3294-0.136-0.054-0.0204-0.3164-0.1664-0.0030.0880.04070.00830.12220.01520.0527-39.113210.017215.3804
41.8128-0.32490.22960.765-0.19191.2950.0341-0.0942-0.03740.01720.0147-0.02850.04620.0663-0.04880.0064-0.0134-0.0010.08-0.01610.0081-16.1825-9.778324.8648
50.92130.1464-0.39860.1516-0.24283.14060.05370.0554-0.1273-0.0292-0.00140.06420.1724-0.2797-0.05230.0365-0.0148-0.02670.1059-0.01230.0752-39.6993-14.92329.9385
62.11081.0047-1.00397.1701-1.3213.39030.01-0.079-0.7411-0.0414-0.0129-0.68260.60810.06080.00280.21950.1236-0.0920.2023-0.00690.3432-40.6249-13.231459.1618
73.43770.65360.33233.08860.50852.54020.0845-0.1776-0.44680.2107-0.0313-0.2770.44170.1548-0.05320.17950.0608-0.06280.13020.02760.1261-47.8679-11.337766.4702
81.33860.36870.222.9608-0.02241.72930.0566-0.0833-0.1510.2015-0.0075-0.01980.3681-0.1695-0.04910.1115-0.0392-0.01730.10870.00440.0212-70.7316-9.358257.5037
91.51530.2385-0.02990.7682-0.04341.56290.02560.09490.0158-0.02550.0649-0.0427-0.03290.1492-0.09050.00640.00820.00120.0852-0.03320.0177-47.626110.139548.4484
101.90580.2876-0.39151.4623-0.09692.32860.01980.05570.2792-0.062-0.00190.075-0.2303-0.1947-0.01790.02920.0346-0.00130.09390.01210.0431-70.957119.494449.4601
111.15682.7575-1.24126.6228-2.72953.39890.1795-0.08350.10590.4541-0.14740.2013-0.31730.1653-0.03210.14020.0364-0.07940.1296-0.08350.1863-64.252726.150155.0223
121.5276-0.25180.42870.1221-0.15753.2562-0.0175-0.1695-0.06080.02490.02080.06850.0218-0.2399-0.00330.03070.01290.01640.0959-0.00260.047-69.512911.403472.6061
136.54933.1135-0.94679.1721-3.03494.14770.1492-0.3260.12260.30040.07060.5206-0.1985-0.4026-0.21980.09490.060.0250.1937-0.01860.0804-80.126918.493271.0124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA5 - 18
2X-RAY DIFFRACTION2ALLA19 - 74
3X-RAY DIFFRACTION3ALLA75 - 160

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