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- PDB-6q9g: Crystal structure of reduced Aquifex aeolicus NADH-quinone oxidor... -

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Basic information

Entry
Database: PDB / ID: 6q9g
TitleCrystal structure of reduced Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE G129D and NuoF bound to NADH
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 (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 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / SLBB domain / de novo design (two linked rop proteins) / 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 ...Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / SLBB domain / de novo design (two linked rop proteins) / 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 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Up-down Bundle / Mainly Alpha / 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 / FOURIER SYNTHESIS / Resolution: 2.1 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 18, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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)138,34222
Polymers134,3104
Non-polymers4,03218
Water17,312961
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,13411
Polymers67,1552
Non-polymers1,9799
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-118 kcal/mol
Surface area21250 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,20711
Polymers67,1552
Non-polymers2,0539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-124 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.330, 116.180, 189.780
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: 18631.656 Da / Num. of mol.: 2 / Mutation: G129D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoE, aq_574 / Plasmid: pETBlue-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O66842, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 48523.301 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: pETBlue-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O66841, NADH dehydrogenase (quinone)

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Non-polymers , 8 types, 979 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / 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: 2.7 Å3/Da / Density % sol: 54.38 % / Mosaicity: 0.4 °
Crystal growTemperature: 281 K / Method: evaporation / pH: 6.75
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.1→26.41 Å / Num. obs: 82411 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.086 / Rrim(I) all: 0.222 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.145.60.92344110.6580.4211.01799.5
10.91-26.46.30.0736400.9970.030.07993

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→26.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.119 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4247 5.2 %RANDOM
Rwork0.1907 ---
obs0.1927 78085 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.59 Å2 / Biso mean: 24.705 Å2 / Biso min: 10.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å2-0 Å2
2--0.59 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 2.1→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9112 0 214 961 10287
Biso mean--21.55 32.73 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178904
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.65213055
X-RAY DIFFRACTIONr_angle_other_deg1.1961.58820724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55851154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77222.662477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.221151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3181552
X-RAY DIFFRACTIONr_chiral_restr0.0620.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021962
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 314 -
Rwork0.278 5640 -
all-5954 -
obs--99.48 %
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)
13.3761-5.6626-1.727413.96824.71861.6692-0.06170.155-0.59090.46710.00820.29260.29230.02380.05350.3541-0.0637-0.01340.21470.02480.379410.3559-18.1503-58.1281
24.1368-2.4782-1.16324.5750.82742.34260.01450.3697-0.48670.0102-0.04330.24220.3703-0.16220.02880.1654-0.0939-0.04910.16850.0260.161913.9826-11.459-62.5763
33.4173-1.9474-0.11814.6384-2.00682.90560.07280.3813-0.3528-0.35650.04130.40720.4494-0.2628-0.1140.2146-0.0473-0.06520.1962-0.05260.10614.4703-8.6221-68.557
42.63761.1244-0.10016.0019-0.80632.43940.0210.1987-0.1742-0.3341-0.01160.13430.34540.0229-0.00940.14030.0386-0.020.17210.00190.024834.4852-8.2962-61.2471
53.53581.32790.7026.22334.15365.129-0.1760.2812-0.2373-0.410.3596-0.3380.31450.633-0.18360.23170.0912-0.00870.2574-0.00110.083342.5591-13.2928-60.6175
61.74380.48060.06374.3371-0.35732.35240.0791-0.0349-0.21030.08590.0022-0.06550.19720.2158-0.08130.08840.0416-0.02450.1657-0.00530.028838.5834-8.0127-52.5075
71.92510.05240.00630.5361-0.20351.3802-0.0281-0.11930.06890.05250.07830.027-0.0972-0.0764-0.05030.0518-0.0058-0.00090.08680.01510.00822.049612.553-48.9829
83.58360.02850.85831.2220.53833.341-0.0680.15450.01-0.04050.0703-0.233-0.01810.4079-0.00230.097-0.00660.01380.1760.00570.048539.831212.1904-73.7718
910.38154.41789.90141.91174.18349.4767-0.323-0.340.6414-0.0592-0.13520.3774-0.3169-0.34980.45820.38120.0870.0430.1773-0.00310.5746-20.447321.8302-14.4601
103.26322.43363.28193.36921.66493.8773-0.1262-0.08490.63940.0394-0.04220.8656-0.2944-0.1080.16840.20640.12890.1910.1694-0.01620.5724-20.48639.3351-13.7983
111.8196-0.0819-0.72430.5341-0.05471.3530.1107-0.45670.54360.14140.02770.173-0.43890.0535-0.13830.2754-0.00860.05020.2201-0.12120.2561-10.05811.8037-6.8626
122.24730.9718-0.82368.77731.80941.9967-0.0154-0.41450.32080.31480.2845-0.6403-0.23950.6215-0.26910.2368-0.0697-0.00360.3467-0.04790.173312.432111.0375-11.9402
132.48470.2591-0.26683.6181-0.55571.66810.236-0.14820.28690.1623-0.01340.0183-0.31290.2387-0.22270.1371-0.03970.03490.1727-0.00420.08293.90697.207-16.864
147.3778-3.2367-2.22353.44793.25375.58180.1328-0.10210.9452-0.35630.2171-0.1309-0.29340.6177-0.34990.1966-0.08930.01910.2824-0.01550.270310.949913.3408-23.5108
152.13550.13620.32390.7315-0.06631.88770.06510.1266-0.0107-0.0378-0.0060.0590.1013-0.0682-0.05910.05180.0397-0.00640.08110.00450.0069-15.5027-9.156-24.5336
160.8466-0.28-0.23220.34290.26693.44580.092-0.0171-0.1443-0.0131-0.0838-0.07990.24160.392-0.00820.0980.0442-0.01020.18060.0350.09877.3312-15.341-10.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 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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