PDB-9fe7: Crystal Structure of oxidized NuoEF variant P228R(NuoF) from Aqui...

ID or keywords:

Entry

Database: PDB / ID: 9fe7

Title

Crystal Structure of oxidized NuoEF variant P228R(NuoF) from Aquifex aeolicus

Components

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

Keywords

ELECTRON TRANSPORT / Complex I / respiratory chain / NADH-ubiquinone oxidoreductase / bioenergetics

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: 2.28 Å

Authors

Wohlwend, D. / Friedrich, T. / Goeppert-Asadollahpour, S.

Funding support

Germany, 1items

Citation

Journal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I).
Authors: Goppert-Asadollahpour, S. / Wohlwend, D. / Friedrich, T.

History

Deposition	May 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9fe7.cif.gz	619.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9fe7.ent.gz	392.7 KB	Display	PDB format
PDBx/mmJSON format	9fe7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fe/9fe7 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/9fe7	HTTPS FTP

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Related structure data

Related structure data	9fdjC 9fdkC 9fdvC 9fe0C 9fe5C 9fe8C 9feaC 9fifC 9fihC 9fiiC 9fijC 9filC 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

Idetical with deposited unit
defined by author&software
Evidence: light scattering, Dimerization of NuoEF to a (NuoEF)2 heterotetramer is the stable assembly in solution

Unit cell

Length a, b, c (Å)	63.283, 116.130, 189.842
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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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(+)::nuoEF_P228R_his / Production host: Escherichia coli (E. coli) / 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 / NADH dehydrogenase I subunit F / NDH-1 subunit F Mass: 48583.379 Da / Num. of mol.: 2 / Mutation: P228R Source method: isolated from a genetically manipulated source Details: The sequence AGHHHHHH is a C-terminal affinity tag used for the affinity purification of the NuoEF complex Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Plasmid: pET-28b(+)::nuoEFhis_P228R / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

#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(+)::nuoEF_P228R_his / Production host:

Escherichia coli (E. coli) / 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 / NADH dehydrogenase I subunit F / NDH-1 subunit F

Mass: 48583.379 Da / Num. of mol.: 2 / Mutation: P228R
Source method: isolated from a genetically manipulated source
Details: The sequence AGHHHHHH is a C-terminal affinity tag used for the affinity purification of the NuoEF complex
Source: (gene. exp.)

Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Plasmid: pET-28b(+)::nuoEFhis_P228R / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 9 types, 755 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.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 11 / 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#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-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#10: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.63 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 100 mM BisTris pH 6.3, 1.65 M ammonium sulfate, 150 mM NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9724 Å / Relative weight: 1
Reflection	Resolution: 2.28→48.001 Å / Num. obs: 63251 / % possible obs: 98 % / Redundancy: 4 % / CC_1/2: 0.982 / R_pim(I) all: 0.089 / Net I/σ(I): 5.7
Reflection shell	Resolution: 2.28→2.34 Å / Num. unique obs: 4468 / CC_1/2: 0.797 / R_pim(I) all: 0.323

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS	VERSION Jan 31, 2020 BUILT=20200131	data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.28→48.001 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.913 / SU B: 14.011 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R: 0.328 / ESU R Free: 0.234
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2443	3160	5.018 %	Random selection
R_work	0.1975	59816	-	-
all	0.2	-	-	-
obs	-	62976	97.293 %	-

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: 23.267 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.186 Å²	0 Å²	-0 Å²
2-	-	2.524 Å²	0 Å²
3-	-	-	-1.337 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→48.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9089	0	161	726	9976

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	9494
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8966
X-RAY DIFFRACTION	r_angle_refined_deg	1.463	1.85	12878
X-RAY DIFFRACTION	r_angle_other_deg	0.513	1.763	20741
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.429	5	1146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.235	5	50
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.908	10	1629
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	15.306	10	16
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.485	10	420
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1362
X-RAY DIFFRACTION	r_chiral_restr_other	0.018	0.2	8
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11064
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2064
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	2032
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	8624
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	4616
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	4553
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	589
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.078	0.2	5
X-RAY DIFFRACTION	r_metal_ion_refined	0.136	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.208	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.19	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	0.472	1.047	4590
X-RAY DIFFRACTION	r_mcbond_other	0.472	1.047	4590
X-RAY DIFFRACTION	r_mcangle_it	0.796	1.881	5734
X-RAY DIFFRACTION	r_mcangle_other	0.796	1.882	5735
X-RAY DIFFRACTION	r_scbond_it	0.844	1.192	4904
X-RAY DIFFRACTION	r_scbond_other	0.794	1.178	4889
X-RAY DIFFRACTION	r_scangle_it	1.32	2.158	7116
X-RAY DIFFRACTION	r_scangle_other	1.269	2.133	7093
X-RAY DIFFRACTION	r_lrange_it	3.094	13.332	40668
X-RAY DIFFRACTION	r_lrange_other	2.905	13.064	40138

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.28-2.339	0.328	193	0.272	4492	0.274	4733	0.893	0.941	98.9858	0.25
2.339-2.403	0.252	236	0.246	4272	0.246	4548	0.954	0.954	99.1205	0.223
2.403-2.473	0.281	236	0.223	4194	0.226	4482	0.947	0.962	98.8398	0.202
2.473-2.548	0.285	221	0.226	4070	0.229	4340	0.94	0.964	98.871	0.205
2.548-2.632	0.264	237	0.22	3949	0.222	4258	0.942	0.965	98.3091	0.199
2.632-2.724	0.29	208	0.215	3781	0.218	4066	0.945	0.968	98.1062	0.193
2.724-2.826	0.276	191	0.202	3634	0.206	3914	0.951	0.972	97.7261	0.182
2.826-2.941	0.258	182	0.191	3528	0.195	3819	0.959	0.975	97.1459	0.173
2.941-3.072	0.265	162	0.192	3414	0.196	3664	0.956	0.975	97.5983	0.176
3.072-3.221	0.26	183	0.197	3199	0.2	3490	0.957	0.975	96.9054	0.183
3.221-3.394	0.252	157	0.192	3111	0.195	3353	0.95	0.977	97.465	0.182
3.394-3.599	0.22	156	0.19	2918	0.192	3144	0.969	0.977	97.7735	0.179
3.599-3.846	0.276	118	0.237	2569	0.239	2991	0.946	0.963	89.8362	0.219
3.846-4.152	0.176	144	0.15	2531	0.151	2801	0.98	0.986	95.5016	0.145
4.152-4.545	0.178	135	0.147	2332	0.148	2585	0.982	0.986	95.4352	0.145
4.545-5.075	0.184	115	0.163	2141	0.164	2343	0.982	0.983	96.2868	0.16
5.075-5.85	0.286	105	0.195	1896	0.2	2085	0.946	0.976	95.9712	0.193
5.85-7.138	0.25	83	0.177	1680	0.18	1808	0.967	0.982	97.5111	0.179
7.138-9.985	0.16	67	0.151	1298	0.151	1412	0.986	0.987	96.6714	0.154
9.985-48.001	0.229	31	0.191	807	0.192	881	0.968	0.977	95.1192	0.196

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	3.863	4.7143	-4.8186	10.1777	-4.8911	7.6192	-0.3171	-0.0568	-0.4448	-0.464	0.2184	-0.2731	0.5511	-0.0791	0.0986	0.2823	0.061	-0.0339	0.2435	-0.0017	0.4208	-10.7846	-19.9816	-35.322
2	3.0337	0.94	-1.9229	2.0241	-0.2045	3.1424	0.0005	-0.3228	-0.4464	0.1413	0.0091	-0.3755	0.4048	0.2446	-0.0096	0.269	0.0938	-0.0591	0.1021	0.0214	0.1585	-13.1033	-10.0132	-30.0283
3	1.2323	0.4926	0.2101	2.3322	0.1784	1.4738	0.0199	-0.1141	-0.2035	0.0984	0.0283	0.0449	0.3438	-0.106	-0.0482	0.2124	-0.0328	-0.0006	0.1039	-0.0006	0.0487	-38.1632	-9.3783	-37.2645
4	2.0738	0.0588	-0.1643	0.5747	0.0741	1.1608	0.0153	0.131	0.1153	-0.066	0.0496	-0.052	-0.0816	0.0357	-0.065	0.1506	0.0007	0.0155	0.0303	-0.0073	0.0186	-21.6945	12.6879	-45.9845
5	2.5959	-0.2934	-0.0283	0.8725	0.1138	3.9394	0.0331	-0.2546	-0.0754	0.0218	-0.0427	0.1109	0.0299	-0.2074	0.0096	0.1608	0.0016	0.0185	0.0509	0.0011	0.0166	-37.0753	10.507	-20.0003
6	6.1161	-0.0736	-1.4799	2.4422	-0.2633	6.0369	0.0325	-0.3304	-0.0915	0.2432	-0.0458	0.4538	-0.1693	-0.4846	0.0133	0.2039	0.0562	0.0276	0.1001	-0.0063	0.0969	-45.7054	18.2954	-24.7708
7	1.4862	-2.0738	1.8742	7.5734	-2.3824	2.9563	-0.17	0.1412	0.6646	0.0431	-0.1941	-0.9693	-0.4121	0.1347	0.3641	0.331	-0.1428	0.087	0.2503	0.0572	0.6857	22.3124	15.5295	-81.091
8	4.6744	-0.8746	-0.4663	3.6888	-0.1316	1.6275	0.1001	0.2638	0.6399	-0.1409	-0.0511	-0.3796	-0.384	0.0804	-0.049	0.2746	-0.0684	0.0458	0.1171	0.0698	0.1764	17.1096	11.2116	-88.7272
9	2.6055	-0.371	0.3058	2.3431	0.1914	1.728	0.0225	0.1244	0.4973	-0.1113	0.0269	0.0211	-0.3936	-0.1952	-0.0494	0.2396	0.0445	0.0179	0.1066	0.0058	0.1244	-6.7104	10.0889	-79.9322
10	2.1956	-0.236	0.6627	0.6527	-0.1778	1.3503	0.0291	-0.1491	-0.0276	0.0038	0.0289	-0.0351	0.0548	0.1164	-0.058	0.1196	-0.0203	-0.0015	0.0429	-0.0099	0.0073	15.7479	-9.6172	-70.1994
11	3.0664	0.4868	1.007	2.0649	-0.1858	3.4179	0.0796	-0.1745	-0.403	0.0326	-0.0573	0.1323	0.3223	-0.2826	-0.0223	0.1547	-0.059	-0	0.0685	0.0159	0.0803	-7.9426	-18.3519	-72.5566
12	4.3471	0.2145	0.2773	1.3645	0.2347	2.683	0.0429	0.1993	0.0589	-0.0953	-0.0414	0.1498	-0.0355	-0.1733	-0.0016	0.136	0.0195	-0.0173	0.0715	0.0017	0.0177	-5.6798	-10.3271	-96.7495
13	6.3827	-0.2592	0.7354	5.0193	0.2034	6.5621	0.4141	0.1912	-0.2382	-0.3021	-0.0466	0.6384	0.4034	-0.7442	-0.3675	0.2117	-0.0753	-0.0351	0.161	0.0065	0.1219	-14.9841	-18.0537	-92.2311

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	5 - 18
2	X-RAY DIFFRACTION	2	ALL	A	19 - 71
3	X-RAY DIFFRACTION	3	ALL	A	72 - 160

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

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Non-polymers , 9 types, 755 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

-Non-polymers , 9 types, 755 molecules

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+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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

-
Non-polymers , 9 types, 755 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi