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- PDB-9hem: Crystal structure of the oxidized respiratory complex I subunit N... -

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Basic information

Entry
Database: PDB / ID: 9hem
TitleCrystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V136M(NuoE), bound to NAD+
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / respiratory chain / cellular respiration / Fe-S-Cluster / flavoprotein
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 / FLAVIN MONONUCLEOTIDE / 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: 2.6 Å
AuthorsWohlwend, D. / Friedrich, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1140/11-2 (SPP 1927) Germany
CitationJournal: To Be Published
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I
Authors: Wohlwend, D. / Gnandt, E. / Vranas, M. / Gerhardt, S. / Friedrich, T.
History
DepositionNov 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: 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)138,45326
Polymers134,2584
Non-polymers4,19522
Water2,756153
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,31113
Polymers67,1292
Non-polymers2,18211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-142 kcal/mol
Surface area21140 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,14213
Polymers67,1292
Non-polymers2,01311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-125 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.723, 63.372, 123.429
Angle α, β, γ (deg.)90.000, 107.258, 90.000
Int Tables number4
Space group name H-MP1211

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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: 18605.684 Da / Num. of mol.: 2 / Mutation: V136M
Source method: isolated from a genetically manipulated source
Details: Mutation V136M was introduced by site-directed mutagenesis
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-28b(+)::nuoEFhis / Production host: Escherichia coli B (bacteria) / 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: 48523.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence AGHHHHHH is a C-terminal affinity tag encoded in the plasmid sequence downstream of the insert, obtained by deleting the original stop codon of the target genes.
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O66841

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Non-polymers , 9 types, 175 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / 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.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BisTris, 1.35-1.45 M ammonium sulfate, 0.1 M NaCl
PH range: 6.25-6.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.6→46.2 Å / Num. obs: 42296 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rpim(I) all: 0.067 / Net I/σ(I): 9.2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4427 / CC1/2: 0.8 / Rpim(I) all: 0.447 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.2 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.889 / SU B: 38.776 / SU ML: 0.385 / Cross valid method: FREE R-VALUE / ESU R: 1.272 / ESU R Free: 0.373
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 2154 5.095 %Random selection
Rwork0.2456 40124 --
all0.248 ---
obs-42278 99.347 %-
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: 43.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.884 Å2-0 Å2-3.318 Å2
2--1.548 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9065 0 196 153 9414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129495
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168907
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.84812893
X-RAY DIFFRACTIONr_angle_other_deg0.4161.76220611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53651139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.76550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99101614
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.2361012
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.09410419
X-RAY DIFFRACTIONr_chiral_restr0.0560.21367
X-RAY DIFFRACTIONr_chiral_restr_other0.0150.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022061
X-RAY DIFFRACTIONr_nbd_refined0.20.22208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.28887
X-RAY DIFFRACTIONr_nbtor_refined0.180.24617
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2339
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1450.26
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.211
X-RAY DIFFRACTIONr_nbd_other0.1660.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.29
X-RAY DIFFRACTIONr_mcbond_it0.7792.3034568
X-RAY DIFFRACTIONr_mcbond_other0.7792.3034568
X-RAY DIFFRACTIONr_mcangle_it1.3224.1435703
X-RAY DIFFRACTIONr_mcangle_other1.3224.1445704
X-RAY DIFFRACTIONr_scbond_it0.9012.4544927
X-RAY DIFFRACTIONr_scbond_other0.8452.434908
X-RAY DIFFRACTIONr_scangle_it1.4444.4987162
X-RAY DIFFRACTIONr_scangle_other1.4064.4577133
X-RAY DIFFRACTIONr_lrange_it3.80628.1340423
X-RAY DIFFRACTIONr_lrange_other3.79628.12240380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.3271750.3672950X-RAY DIFFRACTION99.5857
2.667-2.740.4031490.3312911X-RAY DIFFRACTION100
2.74-2.8190.3541710.3042727X-RAY DIFFRACTION100
2.819-2.9060.3281660.2872733X-RAY DIFFRACTION100
2.906-3.0010.341470.2782629X-RAY DIFFRACTION100
3.001-3.1050.2931360.2682540X-RAY DIFFRACTION99.9626
3.105-3.2220.3261390.2582463X-RAY DIFFRACTION99.9616
3.222-3.3530.3131250.2542374X-RAY DIFFRACTION99.7207
3.353-3.5010.2981040.2312302X-RAY DIFFRACTION99.7926
3.501-3.6710.2951180.2372140X-RAY DIFFRACTION99.6909
3.671-3.8680.256960.2382100X-RAY DIFFRACTION98.5195
3.868-4.1010.2481080.2191921X-RAY DIFFRACTION98.7348
4.101-4.3820.258950.2011832X-RAY DIFFRACTION98.2161
4.382-4.730.27880.1981692X-RAY DIFFRACTION97.4275
4.73-5.1760.229670.2081545X-RAY DIFFRACTION94.6565
5.176-5.7770.207720.2271462X-RAY DIFFRACTION100
5.777-6.6540.268680.2371284X-RAY DIFFRACTION100
6.654-8.1070.314680.2271100X-RAY DIFFRACTION99.9145
8.107-11.2930.277430.234879X-RAY DIFFRACTION99.8917
11.293-46.20.317190.262541X-RAY DIFFRACTION99.8217
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)
11.33760.42880.26863.51560.38030.9617-0.00150.462-0.1165-0.28060.1211-0.6656-0.07730.5053-0.11950.1282-0.0203-0.06150.3953-0.02870.281725.53535.97576.1191
21.7043-0.3031.03552.054-0.6751.84470.0311-0.1263-0.12030.13320.04410.0888-0.0317-0.1297-0.07520.0850.0083-0.08330.0126-0.00060.10916.63647.706420.7186
31.53870.96890.43012.7435-0.49071.0734-0.21080.5564-0.0332-0.68240.2151-0.02870.0170.2622-0.00430.2732-0.0571-0.11870.36640.01160.193662.4659-2.671935.6426
42.0116-0.74511.06322.1594-0.19041.2849-0.1626-0.13120.11190.20250.12620.0796-0.0596-0.09510.03640.06990.0047-0.07370.01610.01730.132952.6342-4.251157.4369
Refinement TLS groupSelection: ALL

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