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

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Basic information

Entry
Database: PDB / ID: 8qgw
TitleCrystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / Respiratory Chain / 3-acetylpridine adenine dinucleotide / NADH-binding
Function / homology
Function and homology information


: / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / 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 / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ...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 / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / 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 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Thioredoxin-like superfamily
Similarity search - Domain/homology
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE / 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: 1.6 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 6, 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

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)138,55430
Polymers134,1944
Non-polymers4,36126
Water21,7801209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17600 Å2
ΔGint-295 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.537, 116.328, 189.621
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: 427AGHHHHHH
Source method: isolated from a genetically manipulated source
Details: Sequence AGHHHHHH was added to the C-terminus via molecular biology techniques 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 , 9 types, 1235 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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#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-A3D / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE


Mass: 662.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1209 / 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: 52.89 %
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: X06DA / Wavelength: 0.9116 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.6→49.627 Å / Num. obs: 185561 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 15.97 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 14.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9111 / CC1/2: 0.729 / Rpim(I) all: 0.429 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimless0.7.9data scaling
REFMAC5.8.0352phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→49.627 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.485 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1872 9369 5.052 %
Rwork0.1618 176080 -
all0.163 --
obs-185449 99.959 %
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: 21.269 Å2
Baniso -1Baniso -2Baniso -3
1-0.013 Å20 Å2-0 Å2
2--0.552 Å20 Å2
3----0.565 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9073 0 220 1209 10502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129696
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168836
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.64913165
X-RAY DIFFRACTIONr_angle_other_deg0.4921.5720657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14951176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.633552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.766101632
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.542109
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.34510427
X-RAY DIFFRACTIONr_chiral_restr0.0730.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021877
X-RAY DIFFRACTIONr_nbd_refined0.2240.21963
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.28246
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24716
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24693
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2980
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2120.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.213
X-RAY DIFFRACTIONr_nbd_other0.1970.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.236
X-RAY DIFFRACTIONr_mcbond_it0.8891.3374668
X-RAY DIFFRACTIONr_mcbond_other0.8891.3374668
X-RAY DIFFRACTIONr_mcangle_it1.3672.0015856
X-RAY DIFFRACTIONr_mcangle_other1.3672.0025857
X-RAY DIFFRACTIONr_scbond_it1.631.5665028
X-RAY DIFFRACTIONr_scbond_other1.5861.5525009
X-RAY DIFFRACTIONr_scangle_it2.5172.287281
X-RAY DIFFRACTIONr_scangle_other2.4562.2597252
X-RAY DIFFRACTIONr_lrange_it5.74622.73611379
X-RAY DIFFRACTIONr_lrange_other5.52319.85210990
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
1.6-1.6420.2756420.262129480.263135930.9450.94799.97790.239
1.642-1.6860.2546720.243125260.243132000.9510.95699.98480.219
1.686-1.7350.2426430.222122190.223128630.9580.96499.99220.195
1.735-1.7890.2186200.205118960.206125160.9650.971000.176
1.789-1.8470.1965790.188115460.188121250.9740.9751000.16
1.847-1.9120.215630.183112090.184117720.9720.9771000.153
1.912-1.9840.2115840.173107670.175113510.9710.981000.146
1.984-2.0650.1865600.161103600.162109210.9770.98399.99080.137
2.065-2.1570.1865650.15799110.159104760.9770.9841000.134
2.157-2.2620.1695160.14695430.147100590.9810.9861000.126
2.262-2.3840.1755130.14290560.14395690.9820.9871000.125
2.384-2.5280.1714620.14286180.14490810.9820.98899.9890.125
2.528-2.7020.1744570.14380740.14585310.9820.9871000.127
2.702-2.9180.1784150.14775790.14979940.9810.9871000.133
2.918-3.1950.1873890.15769630.15973520.9770.9851000.146
3.195-3.570.1993520.15963400.16266930.9780.98699.98510.153
3.57-4.1190.1672640.14256660.14359300.9840.9891000.141
4.119-5.0360.1572570.12748170.12850740.9880.9911000.13
5.036-7.0860.1922190.16537790.16639980.9820.9871000.164
7.086-49.6270.15970.18122630.17923620.9890.98399.91530.182
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)
11.6834-0.55510.37171.0103-0.06411.3540.1080.1178-0.365-0.08920.02250.13290.4875-0.0492-0.13060.1845-0.0305-0.0450.0307-0.0160.083627.1767-10.482-60.0101
20.91740.0334-0.09260.3387-0.12711.59780.0267-0.03420.06320.01340.0488-0.0002-0.0873-0.0248-0.07550.007-0.00090.00290.01170.00110.011225.795512.7774-54.4039
32.3760.5187-0.36680.7695-0.0081.21670.1192-0.15820.51930.0825-0.02920.1266-0.38560.0032-0.090.14050.00860.03580.0317-0.0270.1171-4.229211.0354-12.1967
41.22540.00050.30410.2601-0.05081.28810.08190.0833-0.1172-0.0098-0.00910.00210.08530.0499-0.07280.01230.012-0.00860.0135-0.00660.0136-5.8965-11.9654-18.5479
Refinement TLS groupSelection: ALL

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