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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: Structure / Year: 2026
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.
Authors: Daniel Wohlwend / Thilo Seifermann / Emmanuel Gnandt / Marta Vranas / Stefan Gerhardt / Thorsten Friedrich /
Abstract: Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. ...Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.
History
DepositionNov 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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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