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- PDB-6hl3: wild-type NuoEF from Aquifex aeolicus - oxidized form bound to NAD+ -

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Basic information

Entry
Database: PDB / ID: 6hl3
Titlewild-type NuoEF from Aquifex aeolicus - oxidized form bound to NAD+
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsELECTRON TRANSPORT / Complex I / NuoEF / electron transfer / Aquifex aeolicus
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 / 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 ...Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / NICOTINAMIDE-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 / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGerhardt, S. / Friedrich, T. / Einsle, O. / Gnandt, E. / Schulte, M. / Fiegen, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 2202 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
DepositionSep 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)138,60024
Polymers134,1944
Non-polymers4,40620
Water9,548530
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,43214
Polymers67,0972
Non-polymers2,33512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-140 kcal/mol
Surface area21720 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,16910
Polymers67,0972
Non-polymers2,0728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-127 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.514, 115.759, 189.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (bacteria) / Strain: VF5 / Gene: 63363 / Production host: Escherichia coli (E. coli) / 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
Details: incl. C-terminal 6xHis-tag / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli) / References: UniProt: O66841, NADH dehydrogenase (quinone)

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Non-polymers , 9 types, 550 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#8: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 54.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1 M Tris/HCl 0.1 M Sodium citrate / PH range: 6.9 - 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5479 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5479 Å / Relative weight: 1
ReflectionResolution: 2.036→73.35 Å / Num. obs: 88168 / % possible obs: 97.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 30.02 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 14.4
Reflection shellResolution: 2.036→2.15 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.904 / % possible all: 95.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless(version 0.5.14)data scaling
MOLREPphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE

Resolution: 2.04→73.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9344 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 4365 4.98 %RANDOM
Rwork0.1731 ---
obs0.1746 87576 97.48 %-
Displacement parametersBiso mean: 35.94 Å2
Baniso -1Baniso -2Baniso -3
1--3.1897 Å20 Å20 Å2
2---2.9913 Å20 Å2
3---6.181 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: LAST / Resolution: 2.04→73.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9073 0 234 530 9837
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089537HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9312945HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3307SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes230HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1433HARMONIC5
X-RAY DIFFRACTIONt_it9537HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion17.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1199SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11560SEMIHARMONIC4
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2366 333 5.34 %
Rwork0.2164 5907 -
all0.2175 6240 -
obs--95.49 %
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)
11.10280.5320.09650.4440.00651.26890.17-0.1908-0.30390.1237-0.0233-0.10790.5442-0.0824-0.14670.0993-0.0147-0.113-0.14960.0269-0.079536.0455-10.659659.7178
20.9328-0.03680.28630.37790.16761.90950.0271-0.08910.03280.01160.0139-0.0087-0.0501-0.0586-0.041-0.0630.0179-0.0153-0.1057-0.0197-0.081437.704812.745954.5914
31.3925-0.47090.13420.3598-0.07491.41390.12590.35110.4477-0.1342-0.0562-0.0748-0.5442-0.1691-0.06970.05110.0410.0611-0.11970.0594-0.0954.021311.279312.5386
41.14220.01190.18670.28830.17082.14480.08960.0653-0.08260.0144-0.0185-0.02780.1601-0.1801-0.0711-0.0671-0.0354-0.0084-0.0885-0.0036-0.10875.6116-12.028418.1891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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