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- PDB-8qh4: Crystal structure of reduced respiratory Complex I subunits NuoEF... -

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Basic information

Entry
Database: PDB / ID: 8qh4
TitleCrystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide
Components(NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 2
KeywordsOXIDOREDUCTASE / Complex I / Respiratory Chain / 3-acetylpyridine dinucleotide / NADH-binding
Function / homology
Function and homology information


plasma membrane respiratory chain complex I / 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, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like superfamily
Similarity search - Domain/homology
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-FNR / : / 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: 1.96 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

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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)138,57030
Polymers134,1944
Non-polymers4,37626
Water15,709872
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,24015
Polymers67,0972
Non-polymers2,14313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-188 kcal/mol
Surface area21270 Å2
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,33015
Polymers67,0972
Non-polymers2,23313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-140 kcal/mol
Surface area20900 Å2
Unit cell
Length a, b, c (Å)63.527, 116.619, 190.010
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 (quinone) / 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 / NADH dehydrogenase (quinone)


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, 898 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 872 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
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: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→48.153 Å / Num. obs: 102156 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 14.4
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4996 / CC1/2: 0.864 / Rpim(I) all: 0.318 / % 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: 1.96→48.153 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.161 / SU B: 7.85 / SU ML: 0.112 / Average fsc free: 0.9569 / Average fsc work: 0.9667 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2244 5246 5.181 %
Rwork0.1919 96010 -
all0.194 --
obs-101256 99.166 %
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: 25.256 Å2
Baniso -1Baniso -2Baniso -3
1--0.583 Å2-0 Å2-0 Å2
2--1.355 Å20 Å2
3----0.772 Å2
Refinement stepCycle: LAST / Resolution: 1.96→48.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 214 872 10170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168731
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.65112981
X-RAY DIFFRACTIONr_angle_other_deg0.41.57120399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20851150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.223553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62101618
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg11.351011
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.79510423
X-RAY DIFFRACTIONr_chiral_restr0.0590.21379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
X-RAY DIFFRACTIONr_nbd_refined0.2150.21991
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.28230
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24634
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2753
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.214
X-RAY DIFFRACTIONr_nbd_other0.1460.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1370.21
X-RAY DIFFRACTIONr_mcbond_it0.6661.3614600
X-RAY DIFFRACTIONr_mcbond_other0.6651.3624600
X-RAY DIFFRACTIONr_mcangle_it1.1082.0365750
X-RAY DIFFRACTIONr_mcangle_other1.1082.0375751
X-RAY DIFFRACTIONr_scbond_it0.9721.5434971
X-RAY DIFFRACTIONr_scbond_other0.8911.5164944
X-RAY DIFFRACTIONr_scangle_it1.5732.2717203
X-RAY DIFFRACTIONr_scangle_other1.4772.2287162
X-RAY DIFFRACTIONr_lrange_it5.71120.88211060
X-RAY DIFFRACTIONr_lrange_other5.54719.1610847
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
1.96-2.0110.2613960.24770680.24874640.9520.9571000.209
2.011-2.0660.2623720.23268840.23472570.9510.96399.98620.193
2.066-2.1260.2523810.21666900.21870710.9590.9681000.178
2.126-2.1910.2493590.20565220.20768840.960.97399.95640.168
2.191-2.2630.4553220.41657820.41866520.7940.81591.76190.382
2.263-2.3420.2423370.22158550.22264420.9680.97396.11920.175
2.342-2.430.2263220.17859310.18162530.970.9811000.146
2.43-2.5290.2223030.17656860.17859890.9710.9811000.145
2.529-2.6410.2053140.18154850.18257990.9720.9811000.148
2.641-2.770.2152840.18152330.18355170.9720.981000.151
2.77-2.9190.2272730.17149840.17452580.9720.98299.9810.145
2.919-3.0950.2092510.17847380.17949890.9730.9811000.155
3.095-3.3080.2232680.18744350.18947030.9690.9791000.167
3.308-3.5720.232240.18241730.18543980.9680.98199.97730.164
3.572-3.910.2051870.18338620.18440680.9760.9899.53290.162
3.91-4.3680.1641700.14334950.14436820.9850.98999.53830.133
4.368-5.0370.1751660.14531200.14632860.9840.9891000.136
5.037-6.1520.2031530.16426650.16628180.9780.9871000.151
6.152-8.6310.1661090.15721150.15722240.9860.9871000.148
8.631-48.1530.18550.19312880.19213440.9820.9899.92560.181
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)
12.2848-0.76270.49230.9419-0.04041.63480.19420.1987-0.4724-0.0957-0.01130.15870.5629-0.0142-0.18290.3182-0.016-0.07220.0444-0.02960.105127.2857-10.6863-60.2711
21.37290.0429-0.19330.3684-0.16621.76660.02770.03520.08590.00020.0519-0.0091-0.1038-0.0249-0.07960.0954-0.0099-0.00440.00950.0020.010425.772312.5877-54.5443
32.84520.6289-0.37480.8861-0.03061.44950.1776-0.3060.59810.0773-0.06530.1576-0.45990.0492-0.11240.262-0.00590.0520.0617-0.05560.1303-4.146511.0901-12.5482
41.6655-0.03050.4650.3535-0.08641.53260.10260.024-0.1398-0.007-0.0175-0.00630.12790.0927-0.08510.10730.0276-0.00610.0181-0.00170.0143-5.6849-11.9744-18.6271
Refinement TLS groupSelection: ALL

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