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- PDB-8qh7: Crystal structure of respiratory Complex I subunits NuoEF from Aq... -

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Basic information

Entry
Database: PDB / ID: 8qh7
TitleCrystal structure of respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 3-acetylpyridine adenine dinucleotide (without reducing agent)
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / Respiratory Chain / 3-acetylpyridine adenine dinucleotide / 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
ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED / 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: 1.85 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)138,85132
Polymers134,1944
Non-polymers4,65728
Water19,1861065
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18430 Å2
ΔGint-302 kcal/mol
Surface area41020 Å2
Unit cell
Length a, b, c (Å)63.233, 116.449, 190.047
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(+)::nuoefhis / 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 C-terminus via molecular biology techniques to allow for affinity purification
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoefhis / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O66841

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Non-polymers , 9 types, 1093 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#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-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
#8: Chemical ChemComp-AP0 / ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED


Mass: 664.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 52.82 %
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: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.85→49.7 Å / Num. obs: 120438 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.039 / Net I/σ(I): 13.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5883 / CC1/2: 0.848 / Rpim(I) all: 0.421 / % possible all: 99.9

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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: 1.85→49.695 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.154 / SU B: 6.139 / SU ML: 0.092 / Average fsc free: 0.9695 / Average fsc work: 0.9762 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2006 6201 5.153 %
Rwork0.1708 114143 -
all0.172 --
obs-120344 99.919 %
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: 27.406 Å2
Baniso -1Baniso -2Baniso -3
1-1.063 Å2-0 Å20 Å2
2--0.2 Å2-0 Å2
3----1.263 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9083 0 250 1065 10398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129725
X-RAY DIFFRACTIONr_bond_other_d0.0030.0168875
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.65213200
X-RAY DIFFRACTIONr_angle_other_deg0.4041.57320753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17551171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.766555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.407101647
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.675109
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.80410432
X-RAY DIFFRACTIONr_chiral_restr0.0590.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021894
X-RAY DIFFRACTIONr_nbd_refined0.2090.22027
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.28476
X-RAY DIFFRACTIONr_nbtor_refined0.180.24698
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2867
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.237
X-RAY DIFFRACTIONr_nbd_other0.2090.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3020.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.150.21
X-RAY DIFFRACTIONr_mcbond_it0.7041.5124651
X-RAY DIFFRACTIONr_mcbond_other0.7021.5124651
X-RAY DIFFRACTIONr_mcangle_it1.1152.2635833
X-RAY DIFFRACTIONr_mcangle_other1.1162.2645834
X-RAY DIFFRACTIONr_scbond_it1.1321.7095074
X-RAY DIFFRACTIONr_scbond_other1.1321.715075
X-RAY DIFFRACTIONr_scangle_it1.7812.5057339
X-RAY DIFFRACTIONr_scangle_other1.7812.5067340
X-RAY DIFFRACTIONr_lrange_it6.23132.95642539
X-RAY DIFFRACTIONr_lrange_other5.96731.46841461
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
1.85-1.8980.2884340.27583520.27587920.9460.94999.93180.243
1.898-1.950.2984400.28181220.28285800.940.94499.79020.245
1.95-2.0060.2464350.22779090.22883600.9640.96699.80860.19
2.006-2.0680.2464160.20476770.20681010.9620.97399.90120.169
2.068-2.1360.2164110.18774570.18978680.9690.9771000.156
2.136-2.2110.2024160.17272070.17476280.9740.98299.93450.143
2.211-2.2940.2263840.19769700.19873560.9670.97599.97280.166
2.294-2.3870.1833730.15666780.15770530.9790.98599.97160.131
2.387-2.4930.2053500.15964730.16268250.9760.98599.97070.138
2.493-2.6140.1933530.15861770.1665310.9780.98599.98470.139
2.614-2.7550.1933210.16259150.16462370.9780.98499.9840.144
2.755-2.9220.2193060.16355570.16658640.9710.98499.98290.148
2.922-3.1230.1962930.16752680.16855620.9760.98499.9820.154
3.123-3.3720.2022760.17348960.17551730.9750.98399.98070.165
3.372-3.6920.2052350.16245300.16447850.9750.98699.5820.157
3.692-4.1250.1721950.14241640.14443630.9830.98999.90830.141
4.125-4.7580.1521910.12736670.12938580.9860.9911000.131
4.758-5.8140.1841730.14831440.1533170.9820.9891000.152
5.814-8.1670.1771350.16324740.16426090.9860.9871000.168
8.167-49.6950.164640.18715070.18615710.9880.9811000.197
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)
12.0863-0.77540.39821.012-0.14711.4460.17830.1839-0.4336-0.09460.00850.15390.55980.0265-0.18690.232-0.0315-0.07970.1935-0.02040.100326.9961-10.8166-60.0983
21.08520.013-0.14240.4117-0.23661.7220.0016-0.04420.05880.04430.04450.0034-0.1082-0.0125-0.04610.0163-0.0234-0.00090.1310.010.005525.763412.6639-54.6723
32.61340.6367-0.35450.8089-0.05161.31660.192-0.25860.62430.0769-0.05480.1429-0.46630.098-0.13720.1983-0.0090.06340.1879-0.04810.1536-4.346811.2516-12.5592
41.5016-0.03420.44670.305-0.17081.76470.10210.1046-0.1114-0.0524-0.02940.00160.17470.109-0.07280.04630.0347-0.00590.1316-0.00970.0104-5.8043-11.8281-18.6192
Refinement TLS groupSelection: ALL

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