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- PDB-6q9c: Crystal structure of Aquifex aeolicus NADH-quinone oxidoreductase... -

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Basic information

Entry
Database: PDB / ID: 6q9c
TitleCrystal structure of Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF bound to NADH under anaerobic conditions
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / respiratory chain / complex I / NADH ubiquinone oxidoreductase / Fe-S clusters
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
Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / 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 ...Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / 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 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsWohlwend, D. / Gerhardt, S. / Gnandt, E. / Friedrich, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 1976 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
DepositionDec 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)133,70027
Polymers129,3464
Non-polymers4,35423
Water17,312961
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,83713
Polymers64,6732
Non-polymers2,16411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-122 kcal/mol
Surface area21380 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86414
Polymers64,6732
Non-polymers2,19112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-145 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.279, 115.829, 189.832
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: 17935.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoE, aq_574 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O66842, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 46737.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoF, aq_573 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O66841, NADH dehydrogenase (quinone)

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Non-polymers , 8 types, 984 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-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
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.69 Å3/Da / Density % sol: 54.26 % / Mosaicity: 0.1 °
Crystal growTemperature: 281 K / Method: evaporation / pH: 6.5
Details: (NH4)2SO4, BisTris, NaCl, cryo-protection with glycerol

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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: Nov 24, 2018 / Details: Rh coated meridionally focussing mirror
RadiationMonochromator: Fixed-exit LN2 cooled Double Si (111) Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→49.44 Å / Num. obs: 134290 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.055 / Rrim(I) all: 0.205 / Net I/σ(I): 7.2 / Num. measured all: 1835069 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.8113.81.49866110.8130.4151.555100
9.75-49.4412.20.1059550.9960.0320.1199.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→49.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.936 / SU ML: 0.087 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 6946 5.2 %RANDOM
Rwork0.1795 ---
obs0.1809 127230 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 29.32 Å2 / Biso min: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--1.12 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 1.78→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9104 0 234 961 10299
Biso mean--29.24 40.59 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178921
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.65313063
X-RAY DIFFRACTIONr_angle_other_deg1.2021.58820763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17951154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91322.651479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.353151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4861553
X-RAY DIFFRACTIONr_chiral_restr0.0590.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021961
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 515 -
Rwork0.266 9302 -
all-9817 -
obs--99.96 %
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)
13.4149-5.5237-1.508111.48114.06632.4544-0.00340.012-0.58270.4337-0.13510.4280.62420.05760.13850.322-0.0926-0.02130.25770.07230.416110.3645-18.0007-58.0434
24.0889-1.8972-1.38143.66251.31362.7580.12770.2354-0.5376-0.0947-0.10990.3410.3092-0.1523-0.01770.1977-0.0834-0.06630.15530.01310.182213.9403-11.3169-62.4751
33.5965-0.95850.80533.3907-0.43582.45120.16380.3198-0.4458-0.2341-0.01360.35370.3489-0.1887-0.15020.2275-0.0548-0.06980.1894-0.03810.115614.3916-8.4908-68.4867
42.38260.22220.87813.5577-0.3341.79520.07940.2777-0.36-0.30960.05720.02350.31330.0223-0.13660.18160.0185-0.01970.2031-0.02710.056934.3978-8.0749-61.1809
53.17080.66970.31425.51561.26832.0782-0.06570.2126-0.375-0.30810.162-0.41110.35380.3656-0.09620.24860.0687-0.01410.2298-0.02420.0842.5078-12.9902-60.629
61.3291-0.14690.19753.2203-0.62341.83540.0924-0.0477-0.22210.05630.0166-0.10530.25830.1713-0.1090.13620.0227-0.04070.1846-0.00580.04938.5801-7.8908-52.4498
71.6240.01770.11410.5582-0.0651.2173-0.0156-0.11780.07920.06120.06510.0332-0.0839-0.0686-0.04950.0845-0.01140.00440.1260.01660.010421.924612.6822-48.8912
83.49480.00720.50741.02490.24272.64690.00390.11150.051-0.03720.0208-0.2009-0.0460.3279-0.02470.109-0.02810.01280.15470.00190.040739.747912.3297-73.6868
95.35462.56977.7994.17364.68811.674-0.2112-0.09810.3539-0.0674-0.30370.4097-0.2774-0.22780.51490.35940.03890.02040.2372-0.02210.5384-20.318621.8825-14.1285
104.79571.96542.81353.16861.77773.17270.0143-0.00510.7622-0.0382-0.02590.4306-0.3069-0.14660.01160.18550.0920.07630.12850.01910.2954-20.42469.371-13.5477
112.17180.3158-0.63610.8585-0.16010.93350.1984-0.30930.67640.1555-0.05070.2409-0.36830.0109-0.14770.26920.00730.07050.1939-0.0980.2423-9.983311.7637-6.6259
122.75820.2639-0.19726.8190.66861.34620.0107-0.35210.37560.34060.1725-0.4517-0.22920.3604-0.18320.2066-0.06790.01150.2523-0.02280.134112.460910.9012-11.7038
132.55210.3408-0.20392.4193-0.09730.53320.14130.0510.39310.1901-0.08140.1273-0.20020.1781-0.05990.1506-0.02820.04130.15820.00990.06643.95837.304-16.6473
146.0763-3.0413-0.88625.87670.79223.03010.12130.21370.567-0.1248-0.0830.0931-0.39750.2716-0.03820.1914-0.07380.05290.22710.02850.131211.023213.2474-23.2601
152.08370.16690.16320.70810.0251.73810.07620.2024-0.0538-0.0405-0.00210.06380.084-0.0803-0.07410.08120.0405-0.01430.11240.00030.0117-15.5457-9.0387-24.4051
161.0695-0.2724-0.29490.26090.21993.17560.0830.0416-0.18410.0106-0.0659-0.06980.22720.3233-0.01710.12420.0469-0.01420.15560.01710.10957.2935-15.3648-10.9091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 21
2X-RAY DIFFRACTION2A22 - 51
3X-RAY DIFFRACTION3A52 - 74
4X-RAY DIFFRACTION4A75 - 93
5X-RAY DIFFRACTION5A94 - 121
6X-RAY DIFFRACTION6A122 - 160
7X-RAY DIFFRACTION7B3 - 326
8X-RAY DIFFRACTION8B327 - 419
9X-RAY DIFFRACTION9C8 - 14
10X-RAY DIFFRACTION10C15 - 39
11X-RAY DIFFRACTION11C40 - 90
12X-RAY DIFFRACTION12C91 - 118
13X-RAY DIFFRACTION13C119 - 144
14X-RAY DIFFRACTION14C145 - 160
15X-RAY DIFFRACTION15D3 - 236
16X-RAY DIFFRACTION16D237 - 418

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