PDB-9fdv: Crystal Structure of reduced NuoEF variant R66G(NuoF) from Aquife...

ID or keywords:

Entry

Database: PDB / ID: 9fdv

Title

Crystal Structure of reduced NuoEF variant R66G(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 activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function

Biological species

Aquifex aeolicus VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.986 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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Download

PDBx/mmCIF format	9fdv.cif.gz	626.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9fdv.ent.gz	397.6 KB	Display	PDB format
PDBx/mmJSON format	9fdv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fdv_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	9fdv_full_validation.pdf.gz	2.9 MB	Display
Data in XML	9fdv_validation.xml.gz	50.2 KB	Display
Data in CIF	9fdv_validation.cif.gz	74.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fd/9fdv ftp://data.pdbj.org/pub/pdb/validation_reports/fd/9fdv	HTTPS FTP

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Related structure data

Related structure data	9fdjC 9fdkC 9fe0C 9fe5C 9fe7C 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, The heterodimer of NuoEF forms a stable heterotetramer in solution

Unit cell

Length a, b, c (Å)	63.303, 116.215, 189.543
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 / 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 Mass: 48423.160 Da / Num. of mol.: 2 / Mutation: R66G Source method: isolated from a genetically manipulated source Details: The sequence AGHHHHHH is a C-terminal affinity tag for affinity purification of the complex NuoEF Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+)::nuoEFhis / Production host: Escherichia coli (E. coli) / 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: 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 / 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

Mass: 48423.160 Da / Num. of mol.: 2 / Mutation: R66G
Source method: isolated from a genetically manipulated source
Details: The sequence AGHHHHHH is a C-terminal affinity tag for affinity purification of the complex NuoEF
Source: (gene. exp.)

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

Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O66841

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Non-polymers , 10 types, 885 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.: 8 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 16 / Source method: isolated from a natural source / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#10: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#11: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#12: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.69 Å³/Da / Density % sol: 54.31 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 100 mM BisTris pH 6.3, 1.4 M ammonium sulfate, 100 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: 1.986→49.587 Å / Num. obs: 96723 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC_1/2: 0.994 / R_pim(I) all: 0.066 / Net I/σ(I): 8
Reflection shell	Resolution: 1.986→2.02 Å / Num. unique obs: 4402 / CC_1/2: 0.807 / R_pim(I) all: 0.381

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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
REFMAC	5.8.0425	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.986→49.587 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.951 / SU B: 7.257 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2013	4847	5.016 %	Transfer from scaled data of PDB-ID 9FDJ
R_work	0.1648	91785	-	-
all	0.167	-	-	-
obs	-	96632	99.284 %	-

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: 27.952 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	0 Å²	-0 Å²
2-	-	1.723 Å²	0 Å²
3-	-	-	-1.863 Å²

Refinement step

Cycle: LAST / Resolution: 1.986→49.587 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9100	0	172	849	10121

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	9525
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8976
X-RAY DIFFRACTION	r_angle_refined_deg	1.403	1.846	12931
X-RAY DIFFRACTION	r_angle_other_deg	0.476	1.762	20771
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.055	5	1153
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.067	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.837	10	1619
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	12.556	10	16
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.399	10	419
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1370
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10997
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2063
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1969
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	8412
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	4675
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	4605
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	657
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.081	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.227	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.141	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.186	0.2	28
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.097	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.071	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.875	1.572	4613
X-RAY DIFFRACTION	r_mcbond_other	0.874	1.572	4612
X-RAY DIFFRACTION	r_mcangle_it	1.39	2.82	5765
X-RAY DIFFRACTION	r_mcangle_other	1.39	2.822	5766
X-RAY DIFFRACTION	r_scbond_it	1.511	1.838	4912
X-RAY DIFFRACTION	r_scbond_other	1.438	1.807	4881
X-RAY DIFFRACTION	r_scangle_it	2.421	3.296	7138
X-RAY DIFFRACTION	r_scangle_other	2.338	3.24	7091
X-RAY DIFFRACTION	r_lrange_it	5.796	17.912	10903
X-RAY DIFFRACTION	r_lrange_other	5.624	16.751	10711

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
1.986-2.037	0.268	335	0.264	6436	0.264	7132	0.941	0.937	94.9383	0.233
2.037-2.093	0.271	357	0.245	6507	0.247	6878	0.939	0.948	99.7964	0.215
2.093-2.154	0.244	336	0.225	6392	0.226	6730	0.951	0.958	99.9703	0.195
2.154-2.22	0.231	364	0.196	6178	0.198	6549	0.962	0.97	99.8931	0.167
2.22-2.293	0.218	312	0.193	6045	0.195	6362	0.968	0.972	99.9214	0.167
2.293-2.373	0.211	295	0.171	5852	0.173	6150	0.971	0.979	99.9512	0.15
2.373-2.462	0.212	326	0.166	5610	0.169	5942	0.969	0.981	99.899	0.144
2.462-2.562	0.206	283	0.164	5453	0.166	5738	0.973	0.982	99.9651	0.144
2.562-2.676	0.191	238	0.162	5238	0.163	5478	0.975	0.983	99.9635	0.143
2.676-2.806	0.217	265	0.164	4989	0.167	5261	0.971	0.983	99.8669	0.147
2.806-2.958	0.19	245	0.154	4749	0.155	5024	0.977	0.985	99.4029	0.14
2.958-3.136	0.225	247	0.163	4478	0.166	4763	0.969	0.983	99.2022	0.153
3.136-3.352	0.202	208	0.158	4232	0.16	4485	0.976	0.986	98.9967	0.152
3.352-3.619	0.185	196	0.151	3947	0.153	4181	0.981	0.987	99.0911	0.149
3.619-3.962	0.172	198	0.144	3646	0.145	3885	0.983	0.989	98.9447	0.147
3.962-4.426	0.147	172	0.12	3322	0.122	3509	0.988	0.992	99.5725	0.127
4.426-5.105	0.157	155	0.124	2974	0.126	3140	0.987	0.992	99.6497	0.132
5.105-6.235	0.2	162	0.164	2501	0.166	2675	0.979	0.987	99.5514	0.171
6.235-8.749	0.18	96	0.152	2016	0.153	2119	0.983	0.988	99.6697	0.163
8.749-49.587	0.244	57	0.167	1221	0.17	1288	0.98	0.986	99.2236	0.198

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	6.4805	-6.2711	6.4201	14.264	-4.7676	6.8407	-0.2282	0.2935	0.5393	-0.2608	-0.1257	-0.2534	-0.5776	0.3945	0.3539	0.4148	-0.1028	0.1096	0.1967	-0.0407	0.5068	-10.9355	20.6345	12.1026
2	2.705	-0.8811	0.5843	2.7039	-0.6001	2.5803	0.0992	0.3935	0.6291	-0.1831	-0.1133	-0.3613	-0.3882	0.2142	0.0141	0.1401	-0.0705	0.0666	0.1771	0.058	0.2167	-13.4164	10.4517	7.1857
3	2.9935	-0.4077	-0.1378	2.8254	0.0703	2.1663	0.0647	0.1257	0.4423	-0.1173	-0.0364	0.0206	-0.3882	-0.2525	-0.0284	0.0988	0.0421	0.0224	0.1505	-0.0072	0.0909	-38.5237	10.0589	14.631
4	2.2986	-0.0071	0.3208	0.3751	-0.0388	1.162	0.0553	-0.1635	-0.1221	0.0467	-0.0026	-0.0151	0.125	-0.0396	-0.0527	0.031	-0.0347	-0.0057	0.1043	-0.003	0.0102	-21.9617	-11.605	23.9627
5	4.6593	0.5075	0.0491	0.7235	-0.1158	3.2214	0.0385	0.1404	0.1247	-0.0087	-0.0406	0.11	-0.0099	-0.2183	0.0021	0.0335	0.0118	-0.0084	0.1154	-0.0046	0.0192	-37.399	-10.4909	-2.0405
6	8.7356	0.8765	0.5375	6.0704	0.1562	6.9735	0.2116	0.2176	-0.3013	-0.4134	0.0342	0.677	0.3536	-0.6642	-0.2458	0.1551	-0.0696	-0.0495	0.2178	-0.0029	0.1078	-47.0062	-17.6852	1.9857
7	1.9897	1.8937	-2.0423	9.4453	-4.0302	4.7301	-0.1258	-0.0804	-0.7155	-0.2661	-0.1201	-0.5865	0.7465	0.1145	0.2459	0.2965	0.1305	-0.0666	0.2311	-0.0321	0.414	-40.868	-14.8564	58.4587
8	3.5174	1.5076	0.2031	4.2003	0.5927	1.2259	-0.0019	-0.1961	-0.4873	0.264	-0.0425	-0.3459	0.4037	0.2817	0.0444	0.2297	0.1159	-0.0527	0.1949	0.0232	0.1373	-45.9507	-10.6026	66.0139
9	2.0731	-0.0008	0.1695	3.0314	0.401	2.3827	0.0524	-0.1256	-0.1805	0.192	0.0199	0.0634	0.5315	-0.2379	-0.0723	0.1597	-0.0571	-0.0216	0.1191	0.0045	0.0225	-69.9461	-9.102	57.4099
10	1.91	0.2935	0.1211	0.7408	0.2058	2.4751	-0.0016	0.1191	0.0285	-0.0449	0.0812	-0.0597	-0.0771	0.2202	-0.0796	0.0099	0.0086	-0.0001	0.0959	-0.0334	0.0175	-47.4552	10.6619	47.9418
11	2.4234	0.9014	-0.8113	2.0862	-1.0579	2.9145	-0.0343	-0.0171	0.3369	0.1203	-0.018	0.0632	-0.3294	-0.3184	0.0523	0.0489	0.0544	-0.0234	0.1071	-0.0093	0.0598	-70.8721	19.597	50.6943
12	5.1348	-0.5248	0.0457	0.8983	-0.1614	2.9654	0.0007	-0.139	-0.0932	0.007	0.0343	0.1265	0.0544	-0.2115	-0.035	0.0333	0.01	0.0058	0.1025	0.0041	0.019	-68.6593	10.9109	74.6401
13	7.3001	0.0445	1.7825	8.0597	-0.7755	4.4597	0.1258	-0.3167	0.3866	0.243	0.0017	0.7071	-0.4291	-0.5828	-0.1276	0.134	0.0754	0.0285	0.2023	-0.0222	0.095	-77.9567	18.6082	70.5451

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 , 10 types, 885 molecules

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

-Non-polymers , 10 types, 885 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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Basic information

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Structure visualization

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Downloads & links

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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 , 10 types, 885 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