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- PDB-6saq: wild-type NuoEF from Aquifex aeolicus bound to NADH-OH -

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Basic information

Entry
Database: PDB / ID: 6saq
Titlewild-type NuoEF from Aquifex aeolicus bound to NADH-OH
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsELECTRON TRANSPORT / NADH:ubiquinone Oxidoreductase / Complex I
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 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / SLBB domain / de novo design (two linked rop proteins) / 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 ...Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / SLBB domain / de novo design (two linked rop proteins) / 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 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-L3W / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGerhardt, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation-278002225/RTG 2202 Germany
German Research Foundation-235777276/RTG 1976 Germany
German Research FoundationSPP 1927 Germany
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural Basis for Inhibition of ROS-Producing Respiratory Complex I by NADH-OH.
Authors: Friedrich, T. / Vranas, M. / Wohlwend, D. / Qiu, D. / Gerhardt, S. / Trncik, C. / Pervaiz, M. / Ritter, K. / Steimle, S. / Randazzo, A. / Einsle, O. / Gunther, S. / Jessen, H.J. / Kotlyar, A.
#1: Journal: Nat Commun / Year: 2019
Title: A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I.
Authors: Schulte, M. / Frick, K. / Gnandt, E. / Jurkovic, S. / Burschel, S. / Labatzke, R. / Aierstock, K. / Fiegen, D. / Wohlwend, D. / Gerhardt, S. / Einsle, O. / Friedrich, T.
History
DepositionJul 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)138,20119
Polymers134,1944
Non-polymers4,00715
Water10,899605
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23911
Polymers67,0972
Non-polymers2,1429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-70 kcal/mol
Surface area21120 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9628
Polymers67,0972
Non-polymers1,8656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-71 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.976, 63.794, 121.398
Angle α, β, γ (deg.)90, 105.65, 90
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: 18573.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: contains Iron-sulphur cluster FES
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoE, aq_574 / Production host: Escherichia coli (E. coli)
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: 48523.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: contains FMN, Iron-Sulfur cluster and C-terminal Histag
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli)
References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 6 types, 620 molecules

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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-L3W / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[[(1~{E},3~{Z})-5-azanyl-4-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-methanoyl-amino]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 697.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O16P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8000, Ethylen glycol, 0.1M MES-imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.02→116.9 Å / Num. obs: 92408 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.05 / Net I/σ(I): 11.4
Reflection shellResolution: 2.02→2.13 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 13438 / CC1/2: 0.741 / Rpim(I) all: 0.352

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HLM

6hlm


Resolution: 2.02→29.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.181 4611 -RANDOM
Rwork0.159 ---
obs0.16 92351 99.8 %-
Displacement parametersBiso mean: 37.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.1451 Å20 Å22.6996 Å2
2--0.4238 Å20 Å2
3----3.5689 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.02→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 134 605 9927
Refinement TLS params.

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)
10.574-0.34510.23111.16190.34790.7823-0.05830.32640.09290.32640.0667-0.14610.0929-0.1461-0.0085-0.0188-0.0060.0233-0.03590.0219-0.08712.04541.490123.4294
20.6920.14040.39680.7020.16590.5944-0.0047-0.0039-0.01-0.00390.01290.0603-0.010.0603-0.0082-0.0528-0.00310.0242-0.07860.0118-0.019522.0982-0.46861.8205
31.9177-0.3630.57162.20940.49691.74240.1678-0.43910.0332-0.4391-0.03470.47340.03320.4734-0.1331-0.21950.07080.10770.072-0.0372-0.146246.9928-20.4192-52.9692
41.537-0.31130.67080.8513-0.15391.25540.1108-0.02950.0661-0.0295-0.0206-0.15870.0661-0.1587-0.0903-0.1284-0.00050.0081-0.0546-0.0158-0.125327.7411-21.2604-38.5295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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