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- PDB-9he5: Crystal structure of the oxidized respiratory complex I subunit N... -

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Basic information

Entry
Database: PDB / ID: 9he5
TitleCrystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V90P(NuoE)
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / NADH oxidoreductase / respiratory chain / iron-sulfur-cluster / flavin
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 / 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: 1.844 Å
AuthorsWohlwend, D. / Gerhardt, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1140/11-2 (SPP 1927) Germany
CitationJournal: Structure / Year: 2025
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 13, 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)136,39614
Polymers134,1904
Non-polymers2,20610
Water10,665592
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2218
Polymers67,0952
Non-polymers1,1266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-97 kcal/mol
Surface area21770 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1756
Polymers67,0952
Non-polymers1,0804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-81 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.246, 64.326, 121.576
Angle α, β, γ (deg.)90.000, 106.347, 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: 18571.602 Da / Num. of mol.: 2 / Mutation: V90P
Source method: isolated from a genetically manipulated source
Details: Mutation V90P was introduced by site-directed mutagenesis
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-Blue1::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2
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 not found in the wild-type protein
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-Blue1::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: O66841

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Non-polymers , 6 types, 602 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: 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
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 6.8-7.1, 0.8-1.05 M Na3Citrat, 0.1 M NaCl
PH range: 6.8-7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2012 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→116.661 Å / Num. obs: 122759 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.042 / Rrim(I) all: 0.083 / Net I/σ(I): 13.7
Reflection shellResolution: 1.84→2.06 Å / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.461 / Num. measured all: 129219 / Num. unique obs: 34743 / CC1/2: 0.857 / Rpim(I) all: 0.275 / Rrim(I) all: 0.539 / Net I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.1.29data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.844→116.661 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.69 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 6164 5.022 %Random selection
Rwork0.1678 116572 --
all0.169 ---
obs-122736 99.634 %-
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: 27.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.714 Å20 Å2-1.322 Å2
2--0.391 Å2-0 Å2
3---0.938 Å2
Refinement stepCycle: LAST / Resolution: 1.844→116.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9082 0 98 592 9772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168907
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.85212818
X-RAY DIFFRACTIONr_angle_other_deg0.4561.76420636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.918550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.037101613
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.36710421
X-RAY DIFFRACTIONr_chiral_restr0.0690.21351
X-RAY DIFFRACTIONr_chiral_restr_other0.0240.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022059
X-RAY DIFFRACTIONr_nbd_refined0.2080.21811
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.28026
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24573
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2541
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0560.22
X-RAY DIFFRACTIONr_nbd_other0.1310.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.222
X-RAY DIFFRACTIONr_mcbond_it1.4842.6744578
X-RAY DIFFRACTIONr_mcbond_other1.4842.6744578
X-RAY DIFFRACTIONr_mcangle_it2.2854.8015717
X-RAY DIFFRACTIONr_mcangle_other2.2854.8025718
X-RAY DIFFRACTIONr_scbond_it2.1623.0094866
X-RAY DIFFRACTIONr_scbond_other2.1633.0054843
X-RAY DIFFRACTIONr_scangle_it3.5695.4087070
X-RAY DIFFRACTIONr_scangle_other3.575.3967047
X-RAY DIFFRACTIONr_lrange_it4.8425.94610563
X-RAY DIFFRACTIONr_lrange_other4.77125.5410449
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
1.844-1.8920.3044510.28785540.28890520.9370.94399.48080.266
1.892-1.9440.2834380.2583560.25188070.950.95899.85240.227
1.944-20.2354330.22281560.22385910.9630.96699.97670.2
2-2.0620.2284100.20579220.20683370.9620.97199.940.184
2.062-2.1290.2353940.19476820.19680940.9630.97599.77760.174
2.129-2.2040.2094200.18473750.18578050.9720.97899.87190.162
2.204-2.2870.2163590.17772020.17975870.9710.9899.65730.156
2.287-2.3810.23970.16768370.16972430.9770.98399.87570.146
2.381-2.4860.1673390.15766640.15870070.9810.98599.94290.141
2.486-2.6080.1753330.15763190.15866590.9810.98599.89490.14
2.608-2.7490.1982970.15960850.16163940.9770.98499.81230.145
2.749-2.9150.1793120.15457040.15560330.980.98599.71820.143
2.915-3.1160.1922890.16953570.1756620.9770.98299.71740.16
3.116-3.3660.192550.16850220.16952860.9770.98499.82970.167
3.366-3.6870.172460.16745780.16748680.9860.98599.09610.17
3.687-4.1220.1461980.14141660.14144190.9880.98998.75540.15
4.122-4.7580.1561950.12536620.12639010.9880.99198.87210.141
4.758-5.8250.1751760.1531300.15133400.9860.9998.9820.166
5.825-8.2280.1551470.1524140.1525900.9860.98998.88030.169
8.228-116.6610.223750.16613870.16914870.9770.97898.31880.203

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