PDB-9fea: Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquif...

ID or keywords:

Entry

Database: PDB / ID: 9fea

Title

Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NAD+

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: 1.66 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	9fea.cif.gz	640 KB	Display	PDBx/mmCIF format
PDB format	pdb9fea.ent.gz	405.2 KB	Display	PDB format
PDBx/mmJSON format	9fea.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fea_validation.pdf.gz	4.2 MB	Display	wwPDB validaton report
Full document	9fea_full_validation.pdf.gz	4.2 MB	Display
Data in XML	9fea_validation.xml.gz	54.6 KB	Display
Data in CIF	9fea_validation.cif.gz	82.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fe/9fea ftp://data.pdbj.org/pub/pdb/validation_reports/fe/9fea	HTTPS FTP

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Related structure data

Related structure data	9fdjC 9fdkC 9fdvC 9fe0C 9fe5C 9fe7C 9fe8C 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

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

1

Idetical with deposited unit
defined by author
Evidence: light scattering, The tetrameric assembly of two NuoEF heterodimers into a tetramer is the stable assembly in solution

Unit cell

Length a, b, c (Å)	63.582, 115.785, 190.011
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(+)::nuoEFhis_P228R / 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 Source method: isolated from a genetically manipulated source Details: The C-terminal sequence AGHHHHHH is an artificial affinity tag used for 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(+)::nuoEFhis_P228R / 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
Source method: isolated from a genetically manipulated source
Details: The C-terminal sequence AGHHHHHH is an artificial affinity tag used for 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, 1187 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.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: Chemical	ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₃N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1156 / 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: 52.76 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM BisTris pH 6.5, 1.6 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: 1.66→49.486 Å / Num. obs: 161000 / % possible obs: 97.2 % / Redundancy: 4 % / CC_1/2: 0.993 / R_pim(I) all: 0.064 / Net I/σ(I): 6.9
Reflection shell	Resolution: 1.66→1.69 Å / Num. unique obs: 7841 / CC_1/2: 0.62 / R_pim(I) all: 0.506

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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: 1.66→49.486 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.962 / WR_factor R_free: 0.195 / WR_factor R_work: 0.17 / SU B: 3.815 / SU ML: 0.071 / Average fsc free: 0.9675 / Average fsc work: 0.9721 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1963	7928	4.93 %	Random selection
R_work	0.1729	152870	-	-
all	0.174	-	-	-
obs	-	160798	96.865 %	-

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: 22.061 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.196 Å²	0 Å²	-0 Å²
2-	-	0.732 Å²	0 Å²
3-	-	-	-0.928 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→49.486 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9138	0	211	1156	10505

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	9718
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	9110
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	1.848	13214
X-RAY DIFFRACTION	r_angle_other_deg	0.517	1.766	21072
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.031	5	1173
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.829	5	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.391	10	1655
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	14.795	10	16
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.093	10	436
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1397
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11307
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2147
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	2013
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	8656
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	4744
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	4653
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	908
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.103	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.188	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.175	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.16	0.2	45
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.201	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.951	1.212	4665
X-RAY DIFFRACTION	r_mcbond_other	0.95	1.212	4665
X-RAY DIFFRACTION	r_mcangle_it	1.579	2.171	5847
X-RAY DIFFRACTION	r_mcangle_other	1.579	2.172	5848
X-RAY DIFFRACTION	r_scbond_it	1.614	1.47	5053
X-RAY DIFFRACTION	r_scbond_other	1.565	1.452	5034
X-RAY DIFFRACTION	r_scangle_it	2.56	2.626	7339
X-RAY DIFFRACTION	r_scangle_other	2.487	2.593	7310
X-RAY DIFFRACTION	r_lrange_it	6.046	15.986	11431
X-RAY DIFFRACTION	r_lrange_other	5.876	13.86	11078

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
1.66-1.703	0.308	606	0.297	11120	0.298	12178	0.932	0.938	96.2884	0.288
1.703-1.75	0.278	557	0.265	10830	0.266	11800	0.945	0.953	96.5	0.252
1.75-1.8	0.28	570	0.245	10522	0.247	11500	0.953	0.96	96.4522	0.23
1.8-1.856	0.229	501	0.208	10337	0.209	11229	0.966	0.969	96.5179	0.191
1.856-1.916	0.223	480	0.205	9975	0.206	10839	0.964	0.965	96.4572	0.181
1.916-1.984	0.216	506	0.197	9725	0.198	10528	0.966	0.966	97.179	0.172
1.984-2.058	0.21	472	0.195	9266	0.196	10150	0.968	0.967	95.9409	0.168
2.058-2.142	0.222	478	0.188	9032	0.189	9780	0.966	0.972	97.2393	0.167
2.142-2.237	0.188	438	0.168	8706	0.169	9387	0.977	0.979	97.4113	0.151
2.237-2.346	0.182	442	0.157	8244	0.158	8986	0.978	0.984	96.6615	0.145
2.346-2.473	0.187	423	0.15	7866	0.151	8561	0.978	0.986	96.8228	0.143
2.473-2.622	0.186	373	0.148	7530	0.15	8128	0.98	0.986	97.2318	0.144
2.622-2.803	0.193	374	0.157	7006	0.159	7620	0.976	0.985	96.8504	0.154
2.803-3.027	0.193	335	0.155	6561	0.157	7164	0.976	0.985	96.2591	0.157
3.027-3.314	0.172	326	0.155	6151	0.156	6589	0.982	0.987	98.3002	0.162
3.314-3.704	0.165	278	0.153	5600	0.154	5989	0.985	0.988	98.1466	0.164
3.704-4.273	0.158	277	0.132	4934	0.133	5328	0.986	0.99	97.8041	0.146
4.273-5.223	0.154	224	0.142	4189	0.143	4523	0.99	0.991	97.568	0.163
5.223-7.346	0.229	172	0.199	3319	0.201	3592	0.977	0.983	97.1882	0.221
7.346-49.486	0.23	96	0.223	1958	0.224	2123	0.966	0.972	96.7499	0.254

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	5.53	-5.8025	4.5288	11.6229	-2.5976	4.6865	-0.3573	0.246	0.7121	-0.0882	-0.0879	-0.6545	-0.648	0.3047	0.4452	0.3442	-0.1132	0.0676	0.2293	0.035	0.448	-11.2619	20.7301	12.8211
2	3.1491	-0.6235	0.8178	2.3157	-0.3519	1.8433	0.0788	0.303	0.5378	-0.1864	-0.0748	-0.2784	-0.3225	0.1802	-0.004	0.1412	-0.0526	0.0638	0.1529	0.0679	0.1629	-14.1783	10.45	7.8432
3	2.339	-0.5416	-0.2321	2.5461	0.0635	1.5813	0.057	0.1346	0.3294	-0.136	-0.054	-0.0204	-0.3164	-0.1664	-0.003	0.088	0.0407	0.0083	0.1222	0.0152	0.0527	-39.1132	10.0172	15.3804
4	1.8128	-0.3249	0.2296	0.765	-0.1919	1.295	0.0341	-0.0942	-0.0374	0.0172	0.0147	-0.0285	0.0462	0.0663	-0.0488	0.0064	-0.0134	-0.001	0.08	-0.0161	0.0081	-16.1825	-9.7783	24.8648
5	0.9213	0.1464	-0.3986	0.1516	-0.2428	3.1406	0.0537	0.0554	-0.1273	-0.0292	-0.0014	0.0642	0.1724	-0.2797	-0.0523	0.0365	-0.0148	-0.0267	0.1059	-0.0123	0.0752	-39.6993	-14.9232	9.9385
6	2.1108	1.0047	-1.0039	7.1701	-1.321	3.3903	0.01	-0.079	-0.7411	-0.0414	-0.0129	-0.6826	0.6081	0.0608	0.0028	0.2195	0.1236	-0.092	0.2023	-0.0069	0.3432	-40.6249	-13.2314	59.1618
7	3.4377	0.6536	0.3323	3.0886	0.5085	2.5402	0.0845	-0.1776	-0.4468	0.2107	-0.0313	-0.277	0.4417	0.1548	-0.0532	0.1795	0.0608	-0.0628	0.1302	0.0276	0.1261	-47.8679	-11.3377	66.4702
8	1.3386	0.3687	0.22	2.9608	-0.0224	1.7293	0.0566	-0.0833	-0.151	0.2015	-0.0075	-0.0198	0.3681	-0.1695	-0.0491	0.1115	-0.0392	-0.0173	0.1087	0.0044	0.0212	-70.7316	-9.3582	57.5037
9	1.5153	0.2385	-0.0299	0.7682	-0.0434	1.5629	0.0256	0.0949	0.0158	-0.0255	0.0649	-0.0427	-0.0329	0.1492	-0.0905	0.0064	0.0082	0.0012	0.0852	-0.0332	0.0177	-47.6261	10.1395	48.4484
10	1.9058	0.2876	-0.3915	1.4623	-0.0969	2.3286	0.0198	0.0557	0.2792	-0.062	-0.0019	0.075	-0.2303	-0.1947	-0.0179	0.0292	0.0346	-0.0013	0.0939	0.0121	0.0431	-70.9571	19.4944	49.4601
11	1.1568	2.7575	-1.2412	6.6228	-2.7295	3.3989	0.1795	-0.0835	0.1059	0.4541	-0.1474	0.2013	-0.3173	0.1653	-0.0321	0.1402	0.0364	-0.0794	0.1296	-0.0835	0.1863	-64.2527	26.1501	55.0223
12	1.5276	-0.2518	0.4287	0.1221	-0.1575	3.2562	-0.0175	-0.1695	-0.0608	0.0249	0.0208	0.0685	0.0218	-0.2399	-0.0033	0.0307	0.0129	0.0164	0.0959	-0.0026	0.047	-69.5129	11.4034	72.6061
13	6.5493	3.1135	-0.9467	9.1721	-3.0349	4.1477	0.1492	-0.326	0.1226	0.3004	0.0706	0.5206	-0.1985	-0.4026	-0.2198	0.0949	0.06	0.025	0.1937	-0.0186	0.0804	-80.1269	18.4932	71.0124

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 - 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 , 9 types, 1187 molecules

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

-Non-polymers , 9 types, 1187 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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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

-
Non-polymers , 9 types, 1187 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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

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Jul 12, 2017. Major update of PDB

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Yorodumi