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- PDB-8qg1: Crystal structure of oxidized respiratory Complex I subunits NuoE... -

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Basic information

Entry
Database: PDB / ID: 8qg1
TitleCrystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to ADP-ribose
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / Respiratory Chain / Inhibitor / NADH-binding
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
ADENOSINE-5-DIPHOSPHORIBOSE / 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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsWohlwend, D. / Friedrich, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I.
Authors: Wohlwend, D. / Merono, L. / Bucka, S. / Ritter, K. / Jessen, H.J. / Friedrich, T.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)138,53725
Polymers134,1944
Non-polymers4,34321
Water15,637868
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.129, 116.146, 189.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Plasmid: pET-28b(+) / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(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 / Mutation: AGHHHHHH added after L426
Source method: isolated from a genetically manipulated source
Details: AGHHHHHH were added with molecular biological tehniques to allow for affinity purification
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+) / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O66841

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Non-polymers , 10 types, 889 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-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: 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
#8: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: trisodium citrate, ammonium sulfate, sodium chloride, Tris, BisTris
PH range: 6.3 - 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 EIGER X 16M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.561 Å / Num. obs: 94748 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 13.6 % / Biso Wilson estimate: 31.47 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.039 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4651 / CC1/2: 0.777 / Rpim(I) all: 0.567 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimless0.7.9data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→49.561 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 8.798 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2071 4892 5.168 %
Rwork0.1775 89776 -
all0.179 --
obs-94668 99.685 %
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: 35.457 Å2
Baniso -1Baniso -2Baniso -3
1--0.623 Å2-0 Å20 Å2
2--1.771 Å2-0 Å2
3----1.149 Å2
Refinement stepCycle: LAST / Resolution: 2→49.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9092 0 216 868 10176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168753
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.6513029
X-RAY DIFFRACTIONr_angle_other_deg0.3551.57120455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.298553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.662101623
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg19.781109
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.25210425
X-RAY DIFFRACTIONr_chiral_restr0.0530.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021860
X-RAY DIFFRACTIONr_nbd_refined0.20.22040
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.28485
X-RAY DIFFRACTIONr_nbtor_refined0.180.24686
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2748
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.214
X-RAY DIFFRACTIONr_nbd_other0.1880.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.224
X-RAY DIFFRACTIONr_mcbond_it0.7532.124609
X-RAY DIFFRACTIONr_mcbond_other0.7522.124609
X-RAY DIFFRACTIONr_mcangle_it1.2013.1745763
X-RAY DIFFRACTIONr_mcangle_other1.2013.1755764
X-RAY DIFFRACTIONr_scbond_it1.0352.3024997
X-RAY DIFFRACTIONr_scbond_other0.9992.2794978
X-RAY DIFFRACTIONr_scangle_it1.6523.4037238
X-RAY DIFFRACTIONr_scangle_other1.6053.3667209
X-RAY DIFFRACTIONr_lrange_it5.48131.59911166
X-RAY DIFFRACTIONr_lrange_other5.37728.45510943
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
2-2.0520.33500.29165240.29168910.9290.93299.75330.256
2.052-2.1080.2943640.2664050.26267830.930.94999.79360.225
2.108-2.1690.2653490.24662200.24765780.9490.95699.86320.209
2.169-2.2360.2773290.22860150.2363570.9470.96499.79550.19
2.236-2.3090.2533340.21958260.2261700.9580.96799.83790.183
2.309-2.390.2233080.19357330.19560480.9690.97699.88430.161
2.39-2.480.2143040.18254720.18457830.9730.9899.8790.153
2.48-2.580.2172900.18252200.18355830.9710.9898.69250.15
2.58-2.6950.2072810.17650820.17753650.9740.98299.96270.15
2.695-2.8260.2142680.17148730.17351430.9710.98399.96110.148
2.826-2.9780.1982540.16346600.16549160.9760.98499.95930.144
2.978-3.1580.2092550.17644130.17846680.9720.9821000.16
3.158-3.3750.2072260.18241120.18343390.9740.98199.9770.167
3.375-3.6440.211940.16939010.17140960.9730.98499.97560.158
3.644-3.990.1951740.15636190.15837930.9770.9861000.148
3.99-4.4570.1531690.13732560.13834250.9860.9891000.133
4.457-5.140.1871490.14427890.14630390.9830.98996.67650.141
5.14-6.2780.21450.16724820.16826270.980.9861000.161
6.278-8.8090.161020.15519770.15520790.9860.9871000.153
8.809-49.5610.161470.17611970.17612460.9860.98199.83950.176
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)
12.2353-0.83240.36720.9896-0.04541.85230.14510.2167-0.4695-0.09550.01830.15710.57260.0187-0.16340.3801-0.0165-0.06780.0698-0.0360.106726.9973-10.5759-59.929
21.47140.0401-0.0920.5028-0.20452.10490.02530.0220.10060.01790.0587-0.0035-0.1138-0.0138-0.0840.1719-0.01180.00210.01260.00230.010925.576712.7483-54.2951
33.27010.6995-0.46820.84030.03881.61720.1746-0.29850.71360.0966-0.05970.148-0.51820.0555-0.11490.3586-0.00780.06020.1035-0.03930.1659-4.608211.2144-12.2002
41.9168-0.01230.41930.4532-0.09131.90590.10860.0532-0.1431-0.0087-0.0262-0.01950.13410.1167-0.08240.17690.0266-0.00360.0351-0.00010.0146-5.8116-11.8702-18.5174
Refinement TLS groupSelection: ALL

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