PDB-2qh7: MitoNEET is a uniquely folded 2Fe-2S outer mitochondrial membrane...

ID or keywords:

Entry

Database: PDB / ID: 2qh7

Title

MitoNEET is a uniquely folded 2Fe-2S outer mitochondrial membrane protein stabilized by pioglitazone

Components

Zinc finger CDGSH-type domain 1

Keywords

METAL BINDING PROTEIN /

MitoNEET / 2Fe-2S protein / Outer mitochrodrial membrane protein /

pioglitazone binding

Function / homology

Function and homology information

protein maturation by [2Fe-2S] cluster transfer /

cysteine transaminase / L-cysteine transaminase activity / cytoplasmic side of mitochondrial outer membrane /

regulation of cellular respiration /

regulation of autophagy / 2 iron, 2 sulfur cluster binding /

pyridoxal phosphate binding / mitochondrial outer membrane / membrane => GO:0016020 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.5 Å

Authors

Paddock, M.L. / Wiley, S.E. / Axelrod, H.L. / Cohen, A.E. / Roy, M. / Abresch, E.C. / Capraro, D. / Murphy, A.N. / Nechushtai, R. / Dixon, J.E. / Jennings, P.A.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: MitoNEET is a uniquely folded 2Fe 2S outer mitochondrial membrane protein stabilized by pioglitazone.
Authors: Paddock, M.L. / Wiley, S.E. / Axelrod, H.L. / Cohen, A.E. / Roy, M. / Abresch, E.C. / Capraro, D. / Murphy, A.N. / Nechushtai, R. / Dixon, J.E. / Jennings, P.A.

History

Deposition	Jun 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Feb 21, 2024	Group: 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2qh7.cif.gz	45.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qh/2qh7 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/2qh7	HTTPS FTP

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Related structure data

Similar structure data	1r1c-2 1i53-2 1r1c-3 2z15-2 2z15-4 1ilu-9 5af6-1 3e9v-d 2k8e-d 1i53-1 Search similar-shape structures by Omokage search (details) 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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #144 - Dec 2011 Complex I 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

#117 - Sep 2009
Xanthine Oxidoreductase
similarity (1)
#137 - May 2011
Cytochrome bc1
similarity (1)
#144 - Dec 2011
Complex I
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: Zinc finger CDGSH-type domain 1

B: Zinc finger CDGSH-type domain 1

hetero molecules

18.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.806, 49.621, 59.006
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	LYS	LYS	LYS	LYS	A	A	42 - 106	10 - 74
2	ALA	ALA	GLU	GLU	B	B	43 - 107	11 - 75

#1: Protein	Zinc finger CDGSH-type domain 1 Mass: 8948.327 Da / Num. of mol.: 2 / Fragment: water-solule domain of MitoNEET-residues 33-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1X902, UniProt: Q9NZ45*PLUS
#2: Chemical	ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₂S₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.73 %

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL11-1	1	0.9794
SYNCHROTRON	SSRL	BL9-2	2	1.7374, 1.3624, 1.7418

Detector

Type	ID	Detector	Date
MARMOSAIC 325 mm CCD	1	CCD	Mar 22, 2007
MARMOSAIC 325 mm CCD	2	CCD	Apr 10, 2007

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	1.7374	1
3	1.3624	1
4	1.7418	1

Reflection

D res high: 1.8 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res low (Å)	Num. obs	% possible obs
11.7	1	5.1	151046	0.08	0.08	59.028	12921	95.9
13.4	2	6.2	179865	0.066	0.066	50.063	13465	99.6
11.6	3	5.3	150328	0.078	0.078	59.131	12904	95.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
8.05	59.03	90.1	1	0.054	0.054	8.9
5.69	8.05	99.6	1	0.059	0.059	11.9
4.65	5.69	100	1	0.058	0.058	12.7
4.03	4.65	100	1	0.065	0.065	13.2
3.6	4.03	100	1	0.069	0.069	13.3
3.29	3.6	100	1	0.072	0.072	13.4
3.04	3.29	100	1	0.078	0.078	13.5
2.85	3.04	100	1	0.086	0.086	13.5
2.68	2.85	100	1	0.091	0.091	13.5
2.55	2.68	100	1	0.102	0.102	13.4
2.43	2.55	100	1	0.109	0.109	13.3
2.32	2.43	100	1	0.124	0.124	13.3
2.23	2.32	100	1	0.14	0.14	13.3
2.15	2.23	100	1	0.155	0.155	13.3
2.08	2.15	100	1	0.186	0.186	13.2
2.01	2.08	100	1	0.228	0.228	13.3
1.95	2.01	99.6	1	0.258	0.258	10
1.9	1.95	98.1	1	0.291	0.291	7
1.85	1.9	85.4	1	0.37	0.37	5.6
1.8	1.85	63.4	1	0.455	0.455	4.7
8.05	50.06	80.7	2	0.058	0.058	7
5.69	8.05	96.9	2	0.056	0.056	10.3
4.65	5.69	97.1	2	0.051	0.051	11.1
4.02	4.65	99	2	0.052	0.052	11.7
3.6	4.02	100	2	0.056	0.056	12.3
3.29	3.6	100	2	0.058	0.058	13.1
3.04	3.29	100	2	0.059	0.059	13.5
2.85	3.04	100	2	0.063	0.063	13.6
2.68	2.85	100	2	0.066	0.066	13.8
2.55	2.68	100	2	0.072	0.072	13.7
2.43	2.55	100	2	0.075	0.075	13.8
2.32	2.43	100	2	0.081	0.081	13.8
2.23	2.32	100	2	0.085	0.085	13.7
2.15	2.23	100	2	0.09	0.09	13.9
2.08	2.15	100	2	0.106	0.106	13.8
2.01	2.08	100	2	0.121	0.121	13.7
1.95	2.01	100	2	0.131	0.131	13.8
1.9	1.95	100	2	0.151	0.151	13.7
1.85	1.9	100	2	0.171	0.171	13.7
1.8	1.85	100	2	0.196	0.196	13.7
8.05	59.13	90.1	3	0.052	0.052	9
5.69	8.05	100	3	0.058	0.058	11.9
4.65	5.69	100	3	0.057	0.057	12.7
4.02	4.65	100	3	0.063	0.063	13.2
3.6	4.02	100	3	0.067	0.067	13.3
3.29	3.6	100	3	0.068	0.068	13.4
3.04	3.29	100	3	0.075	0.075	13.5
2.85	3.04	100	3	0.083	0.083	13.5
2.68	2.85	100	3	0.09	0.09	13.5
2.55	2.68	100	3	0.101	0.101	13.4
2.43	2.55	100	3	0.108	0.108	13.3
2.32	2.43	100	3	0.127	0.127	13.4
2.23	2.32	100	3	0.142	0.142	13.3
2.15	2.23	100	3	0.163	0.163	13.3
2.08	2.15	100	3	0.195	0.195	13.2
2.01	2.08	100	3	0.245	0.245	13.1
1.95	2.01	99.4	3	0.281	0.281	9.6
1.9	1.95	97.7	3	0.324	0.324	6.8
1.85	1.9	84.2	3	0.394	0.394	5.5
1.8	1.85	60.9	3	0.504	0.504	4.6

Reflection

Resolution: 1.5→38 Å / Num. obs: 21479 / % possible obs: 94.7 % / B_iso Wilson estimate: 27.683 Å² / R_merge(I) obs: 0.058 / Net I/σ(I): 30.92

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique all	% possible all
1.5-1.55		0.754	3.2	15789	1392	66.8
1.55-1.62		0.633	4.3	30876	2091	83.7
1.62-1.69		0.484	6.4	37206	2005	95.7
1.69-1.78		0.403	10.3	63799	2257	100
1.78-1.89		0.305	15.1	72121	2220	100
1.89-2.04		0.205	22.4	76928	2306	100
2.04-2.24		0.132	33.2	74956	2188	100
2.24-2.56		0.085	47.9	77006	2256	100
	2.56	0.054	65.4	79179	2331	100

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	1.7374	2.45	-7.96
1	3 wavelength	2	1.3624	2.6	-0.3
1	3 wavelength	3	1.7418	2.45	-7.96

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Fe	17.639	0.663	0.135	0.145	0.611
2	Fe	17.437	0.706	0.858	0.09	0.648
3	Fe	17.685	0.691	0.159	0.179	0.583

Phasing dm

FOM : 0.73 / FOM acentric: 0.74 / FOM centric: 0.71 / Reflection: 13466 / Reflection acentric: 11564 / Reflection centric: 1902

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.1-38.189	0.94	0.97	0.89	628	423	205
3.2-5.1	0.94	0.96	0.87	1845	1476	369
2.6-3.2	0.9	0.91	0.83	2270	1932	338
2.3-2.6	0.86	0.87	0.8	2263	1971	292
1.9-2.3	0.7	0.71	0.58	3987	3540	447
1.8-1.9	0.33	0.34	0.24	2473	2222	251

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SOLVE	2.12	phasing
RESOLVE	2.12	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
Blu-Ice		data collection
MOSFLM		data reduction
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.5→38 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.954 / SU B: 4.564 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.ELECTRON DENSITIES CORRESPONDING TO RESIDUES 33-41 AND 107-108 ON THE A SUBUNIT AND ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.223	1081	5 %	RANDOM
R_work	0.182	-	-	-
obs	0.184	21479	95.25 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 33.279 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.95 Å²	0 Å²	0 Å²
2-	-	1.35 Å²	0 Å²
3-	-	-	-2.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1028	0	8	128	1164

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	1101
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	958
X-RAY DIFFRACTION	r_angle_refined_deg	1.717	1.936	1485
X-RAY DIFFRACTION	r_angle_other_deg	0.92	3	2254
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.444	5	139
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.957	25	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.99	15	198
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	5.394	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	153
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1227
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	211
X-RAY DIFFRACTION	r_nbd_refined	0.182	0.3	175
X-RAY DIFFRACTION	r_nbd_other	0.172	0.3	936
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.5	503
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.5	600
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.5	174
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.116	0.3	6
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.204	0.3	20
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.135	0.5	11
X-RAY DIFFRACTION	r_mcbond_it	1.843	3	726
X-RAY DIFFRACTION	r_mcbond_other	0.528	3	275
X-RAY DIFFRACTION	r_mcangle_it	2.309	5	1076
X-RAY DIFFRACTION	r_scbond_it	3.745	8	472
X-RAY DIFFRACTION	r_scangle_it	4.654	11	401

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 917 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
LOOSE POSITIONAL	0.25	5
LOOSE THERMAL	1.51	10

LS refinement shell

Resolution: 1.5→1.542 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.426	48	-
R_work	0.366	1121	-
obs	-	1169	71.28 %

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	1.9164	-0.2153	-1.487	2.0161	-0.2902	7.0724	-0.136	0.0005	-0.1437	-0.0486	-0.1035	-0.1278	0.4781	0.2602	0.2395	-0.1435	0.0307	0.0168	-0.2042	0.0219	-0.138	11.9394	45.1101	7.8926
2	3.2473	0.1712	-1.9405	1.9235	0.4046	8.1164	-0.0359	0.0856	0.2158	-0.0118	-0.0608	-0.0868	-0.4634	0.1792	0.0967	-0.1802	0.0481	-0.0158	-0.2361	0.0328	-0.1209	10.8026	54.5578	5.6189

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	42 - 106	10 - 74
2	X-RAY DIFFRACTION	2	B	B	43 - 107	11 - 75

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