PDB-9hen: Crystal structure of the oxidized respiratory complex I subunit N...

ID or keywords:

Entry

Database: PDB / ID: 9hen

Title

Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, double mutation V90P and V136M(NuoE), bound to NAD+

Components

(NADH-quinone oxidoreductase subunit ...) x 2

Keywords

OXIDOREDUCTASE / Complex I / respiratory chain / cellular respiration / Fe-S-Cluster / flavoprotein

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

Biological species

Aquifex aeolicus VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.27 Å

Authors

Wohlwend, D. / Friedrich, T.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I
Authors: Wohlwend, D. / Gnandt, E. / Vranas, M. / Gerhardt, S. / Friedrich, T.

History

Deposition	Nov 14, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9hen.cif.gz	628 KB	Display	PDBx/mmCIF format
PDB format	pdb9hen.ent.gz	398.6 KB	Display	PDB format
PDBx/mmJSON format	9hen.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hen_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	9hen_full_validation.pdf.gz	3 MB	Display
Data in XML	9hen_validation.xml.gz	55.4 KB	Display
Data in CIF	9hen_validation.cif.gz	77.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/9hen ftp://data.pdbj.org/pub/pdb/validation_reports/he/9hen	HTTPS FTP

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Related structure data

Related structure data	52895C 52969C 52970C 52971C 52973C 9he5C 9hegC 9hemC 9q8iC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#144 - Dec 2011 Complex I similarity (19) #117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #36 - Dec 2002 Cytochrome c similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#144 - Dec 2011
Complex I
similarity (19)
#117 - Sep 2009
Xanthine Oxidoreductase
similarity (1)
#137 - May 2011
Cytochrome bc1
similarity (1)
#111 - Mar 2009
Hydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#36 - Dec 2002
Cytochrome c
similarity (1)
#82 - Oct 2006
Cytochrome p450
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

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

138 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADH-quinone oxidoreductase subunit E

B: NADH-quinone oxidoreductase subunit F

hetero molecules

defined by author&software
Evidence: light scattering, In solution, NuoEF forms a (AB)2 heterotetramer composed of two copies of the NuoEF heterodimer occuring in native complex I
68.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: NADH-quinone oxidoreductase subunit E

D: NADH-quinone oxidoreductase subunit F

hetero molecules

defined by author&software
69 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.878, 64.190, 124.115
Angle α, β, γ (deg.)	90.000, 107.744, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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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: 18603.666 Da / Num. of mol.: 2 / Mutation: V90P, V136M Source method: isolated from a genetically manipulated source Details: Mutations V90P and V136M were introduced by site-directed mutagenesis Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-28b(+)::nuoE_VPVM_Fhis / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta2 (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 Source method: isolated from a genetically manipulated source Details: The sequence AGHHHHHH is a C-terminal affinity tag introduced by the plasmid after deleting the native stop codon of nuoF Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoE_VPVM_Fhis / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O66841

#1: Protein

NADH-quinone oxidoreductase subunit E / NADH dehydrogenase I subunit E / NDH-1 subunit E

Mass: 18603.666 Da / Num. of mol.: 2 / Mutation: V90P, V136M
Source method: isolated from a genetically manipulated source
Details: Mutations V90P and V136M were introduced by site-directed mutagenesis
Source: (gene. exp.)

Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-28b(+)::nuoE_VPVM_Fhis / Production host:

Escherichia coli B (bacteria) / Strain (production host): Rosetta2 (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
Source method: isolated from a genetically manipulated source
Details: The sequence AGHHHHHH is a C-terminal affinity tag introduced by the plasmid after deleting the native stop codon of nuoF
Source: (gene. exp.)

Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoE_VPVM_Fhis / Production host:

Escherichia coli B (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O66841

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Non-polymers , 8 types, 737 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-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical	ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#9: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.07 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.1 M BisTris, 1.35-1.45 M ammonium sulfate, 0.1 M NaCl PH range: 6.25-6.75

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.27→48.24 Å / Num. obs: 66804 / % possible obs: 99.1 % / Redundancy: 7 % / CC_1/2: 0.998 / R_pim(I) all: 0.044 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2.27→2.32 Å / Num. unique obs: 4467 / CC_1/2: 0.857 / R_pim(I) all: 0.286

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.27→48.24 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.949 / SU B: 8.14 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.249 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1825	3322	4.975 %	Random selection
R_work	0.1621	63446	-	-
all	0.163	-	-	-
obs	-	66768	98.869 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.796 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.395 Å²	-0 Å²	-0.806 Å²
2-	-	0.327 Å²	0 Å²
3-	-	-	1.314 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→48.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9144	0	173	723	10040

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	9654
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9093
X-RAY DIFFRACTION	r_angle_refined_deg	1.126	1.853	13113
X-RAY DIFFRACTION	r_angle_other_deg	0.397	1.766	21054
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.627	5	1164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.818	5	53
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.344	10	1661
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	19.422	10	16
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.525	10	428
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	1384
X-RAY DIFFRACTION	r_chiral_restr_other	0.013	0.2	8
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	11268
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2106
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	1931
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	8443
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	4655
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	4479
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	532
X-RAY DIFFRACTION	r_metal_ion_refined	0.068	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.142	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.156	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.102	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.856	1.739	4644
X-RAY DIFFRACTION	r_mcbond_other	0.856	1.738	4644
X-RAY DIFFRACTION	r_mcangle_it	1.522	3.12	5812
X-RAY DIFFRACTION	r_mcangle_other	1.522	3.122	5813
X-RAY DIFFRACTION	r_scbond_it	1.038	1.92	5010
X-RAY DIFFRACTION	r_scbond_other	1.038	1.92	5011
X-RAY DIFFRACTION	r_scangle_it	1.737	3.486	7273
X-RAY DIFFRACTION	r_scangle_other	1.737	3.486	7274
X-RAY DIFFRACTION	r_lrange_it	4.373	21.626	41310
X-RAY DIFFRACTION	r_lrange_other	4.246	21.209	40760

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.27-2.329	0.259	232	0.225	4666	X-RAY DIFFRACTION	99.2905
2.329-2.393	0.21	241	0.191	4539	X-RAY DIFFRACTION	99.2731
2.393-2.462	0.193	220	0.178	4432	X-RAY DIFFRACTION	99.0841
2.462-2.537	0.18	231	0.17	4287	X-RAY DIFFRACTION	98.7757
2.537-2.62	0.19	213	0.169	4110	X-RAY DIFFRACTION	98.429
2.62-2.712	0.194	209	0.169	4030	X-RAY DIFFRACTION	98.5356
2.712-2.814	0.177	211	0.159	3821	X-RAY DIFFRACTION	97.6981
2.814-2.928	0.204	212	0.16	3693	X-RAY DIFFRACTION	97.2361
2.928-3.058	0.197	195	0.166	3622	X-RAY DIFFRACTION	99.7648
3.058-3.207	0.194	183	0.175	3458	X-RAY DIFFRACTION	99.7808
3.207-3.379	0.195	163	0.176	3298	X-RAY DIFFRACTION	99.6832
3.379-3.583	0.197	159	0.174	3146	X-RAY DIFFRACTION	99.7585
3.583-3.829	0.166	150	0.175	2905	X-RAY DIFFRACTION	98.8353
3.829-4.134	0.168	151	0.142	2747	X-RAY DIFFRACTION	99.5876
4.134-4.525	0.127	134	0.123	2504	X-RAY DIFFRACTION	99.3223
4.525-5.054	0.137	113	0.126	2274	X-RAY DIFFRACTION	97.7077
5.054-5.825	0.201	91	0.158	1994	X-RAY DIFFRACTION	95.9062
5.825-7.108	0.17	96	0.161	1730	X-RAY DIFFRACTION	100
7.108-9.945	0.148	76	0.128	1362	X-RAY DIFFRACTION	99.9305
9.945-48.24	0.264	42	0.193	828	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.0674	-2.3181	-1.3065	4.6737	0.4416	3.13	0.0496	0.5948	0.3277	-0.5914	-0.0024	-0.6886	-0.4226	0.6135	-0.0472	0.2809	-0.1368	0.1291	0.5583	0.0775	0.3559	1.9203	18.8928	-52.947
2	3.8245	-0.2491	-1.1577	5.2277	-0.2157	9.0782	0.021	0.1658	0.0712	-0.2033	0.051	-0.6847	-0.099	0.6385	-0.072	0.1449	-0.0555	0.079	0.4562	0.0255	0.4004	5.9049	17.3574	-44.3528
3	3.0269	0.6698	-0.5546	4.1039	-0.5845	3.9861	0.1274	0.6047	-0.3071	-0.6137	-0.1465	-0.7283	0.3781	0.5484	0.0191	0.2892	0.1408	0.0966	0.4618	-0.0716	0.2812	-0.6987	-7.0823	-54.1139
4	1.3977	-0.4543	0.2484	2.1221	0.1321	2.1761	0.0423	0.2599	0.0003	-0.2592	-0.0241	0.1451	-0.0617	-0.1696	-0.0182	0.0645	-0.004	-0.0246	0.2174	0.0203	0.0701	-26.6004	10.7455	-44.9739
5	2.3731	-0.7781	0.821	2.4333	0.2749	2.1371	-0.0589	0.1112	0.1101	-0.0327	0.0034	-0.0043	-0.162	-0.0186	0.0555	0.0919	0.006	0.0003	0.1506	0.0213	0.0257	-20.1148	14.4598	-41.9016
6	3.0487	0.1605	2.0616	0.9891	0.0134	1.5948	0.2834	-0.0436	-0.4415	0.0163	-0.0327	-0.0046	0.3463	-0.0918	-0.2507	0.1774	-0.0155	-0.0351	0.1973	-0.0167	0.1449	-13.0841	-11.3116	-32.2449
7	4.2054	-1.05	1.013	4.5997	-3.0822	6.2074	-0.1289	0.5721	-0.2731	-0.8234	-0.1544	-0.3855	0.3995	0.6866	0.2833	0.3041	0.0074	0.0395	0.2138	-0.1076	0.18	38.7192	-22.6055	-24.4519
8	5.8067	2.4885	-1.4682	4.3514	-2.5672	3.188	-0.1555	0.4158	-0.1613	-0.8449	0.1067	-0.0512	0.2257	0.0928	0.0488	0.3277	0.0007	-0.022	0.2475	-0.0668	0.1035	31.8859	-17.6221	-29.2122
9	3.552	0.3334	-0.3504	2.5576	-0.4885	1.9575	-0.1015	0.3989	0.0025	-0.4569	-0.0119	0.0434	-0.0852	0.0476	0.1134	0.1227	-0.0153	-0.0264	0.0896	0.0263	0.0686	37.4883	5.1918	-20.449
10	0.9909	-0.036	0.4323	1.7831	-0.2623	1.4045	0.0429	0.012	-0.12	0.0146	0.0055	0.0925	0.0434	-0.0623	-0.0484	0.0104	-0.0004	0.0074	0.008	-0.0099	0.0545	33.1979	-18.132	0.3345
11	2.903	0.058	2.2387	0.5312	0.327	2.4847	-0.1438	-0.2168	0.2979	0.0158	-0.0038	0.1995	-0.2066	-0.2758	0.1475	0.0686	0.032	0.0099	0.0768	-0.0113	0.1739	17.6471	4.9941	-3.8006

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 45
2	X-RAY DIFFRACTION	2	ALL	A	46 - 74
3	X-RAY DIFFRACTION	3	ALL	A	75 - 160

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NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD

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Non-polymers , 8 types, 737 molecules

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-NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD

-Non-polymers , 8 types, 737 molecules

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-Experimental details

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-Sample preparation

-Data collection

-Processing

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-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

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NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD

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Non-polymers , 8 types, 737 molecules

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Details

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