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- PDB-6hli: wild-type NuoEF from Aquifex aeolicus - reduced form bound to NAD+ -

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Basic information

Entry
Database: PDB / ID: 6hli
Titlewild-type NuoEF from Aquifex aeolicus - reduced form bound to NAD+
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsELECTRON TRANSPORT / Complex I / NuoEF / electron transfer / Aquifex aeolicus
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 / 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 ...Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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 / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsGerhardt, S. / Friedrich, T. / Einsle, O. / Gnandt, E. / Schulte, M. / Fiegen, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 2202 Germany
CitationJournal: 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
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / software
Item: _software.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)137,48812
Polymers134,1944
Non-polymers3,2948
Water4,468248
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7446
Polymers67,0972
Non-polymers1,6474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-80 kcal/mol
Surface area21360 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7446
Polymers67,0972
Non-polymers1,6474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-79 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.590, 116.040, 189.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Production host: Escherichia coli (E. coli) / References: UniProt: O66842, NADH dehydrogenase (quinone)
#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: Sequence contains C-terminal 6xHis Expressions-tag / Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli) / References: UniProt: O66841, NADH dehydrogenase (quinone)

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Non-polymers , 5 types, 256 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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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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: 52.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1M Tris/HCl 0.1M Sodium citrate / PH range: 6.9 - 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 2016 / Details: VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.38→116 Å / Num. obs: 57523 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.051 / Rsym value: 0.119 / Net I/σ(I): 13.2
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8284 / CC1/2: 0.778 / Rpim(I) all: 0.351 / Rsym value: 0.757 / % possible all: 100

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Processing

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

Resolution: 2.38→60.3 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.23
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2830 4.95 %RANDOM
Rwork0.205 ---
obs0.206 57156 99.8 %-
Displacement parametersBiso mean: 50.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.5624 Å20 Å20 Å2
2---9.6305 Å20 Å2
3---8.068 Å2
Refinement stepCycle: 1 / Resolution: 2.38→60.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9095 0 174 248 9517
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019509HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0412903HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3299SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes230HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1437HARMONIC5
X-RAY DIFFRACTIONt_it9509HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion18.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1201SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11296SEMIHARMONIC4
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2626 204 4.87 %
Rwork0.2141 3983 -
all0.2165 4187 -
obs--100 %
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)
11.55420.54960.13160.61880.09871.80150.0703-0.4226-0.2570.1515-0.026-0.11410.5442-0.1681-0.04430.1431-0.0344-0.1012-0.12820.0257-0.156335.9413-10.628560.0599
21.4871-0.00440.26680.7360.29682.84540.0195-0.2720.1813-0.004-0.02170.0278-0.1297-0.21340.0021-0.08620.0135-0.0616-0.1881-0.0932-0.095237.743312.616454.591
31.01070.17250.35860.8131-0.01892.15640.03230.48570.496-0.173-0.0807-0.1116-0.5442-0.25580.04840.11660.0997-0.0263-0.17670.1235-0.09754.045810.95112.4083
42.05680.18310.49970.07040.35673.18650.12110.2439-0.01760.0172-0.0609-0.03210.2638-0.3007-0.0601-0.0122-0.034-0.0603-0.147-0.0092-0.16915.6814-12.192918.3686
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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