PDB-8qns: Crystal structure of murine AIF bound to N-terminal domain of CHCHD4

ID or keywords:

Entry

Database: PDB / ID: 8qns

Title

Crystal structure of murine AIF bound to N-terminal domain of CHCHD4

Components

Apoptosis-inducing factor 1, mitochondrial
Mitochondrial intermembrane space import and assembly protein 40

Keywords

PROTEIN BINDING / apoptosis inducing factor / mitochondrial protein / FAD / NAD / protein complex / flavoprotein / Rossmann fold topology

Function / homology

Function and homology information

'de novo' post-translational protein folding / peptidyl-cysteine oxidation / electron-transferring-flavoprotein dehydrogenase activity / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / positive regulation of cellular respiration / establishment of protein localization to mitochondrion / NAD(P)H oxidase H2O2-forming activity ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.206 Å

Authors

Fagnani, E. / Milani, M.

Funding support

European Union, 1items

Citation

Journal: Structure / Year: 2024
Title: CHCHD4 binding affects the active site of apoptosis inducing factor (AIF): Structural determinants for allosteric regulation.
Authors: Fagnani, E. / Cocomazzi, P. / Pellegrino, S. / Tedeschi, G. / Scalvini, F.G. / Cossu, F. / Da Vela, S. / Aliverti, A. / Mastrangelo, E. / Milani, M.

History

Deposition	Sep 27, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qns.cif.gz	946.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8qns.ent.gz	611.5 KB	Display	PDB format
PDBx/mmJSON format	8qns.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qns_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	8qns_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8qns_validation.xml.gz	67.5 KB	Display
Data in CIF	8qns_validation.cif.gz	90.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/8qns ftp://data.pdbj.org/pub/pdb/validation_reports/qn/8qns	HTTPS FTP

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Related structure data

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	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (3) #154 - Oct 2012 Citric Acid Cycle similarity (3) #36 - Dec 2002 Cytochrome c similarity (1) #5 - May 2000 Cytochrome c Oxidase similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Apoptosis-inducing factor 1, mitochondrial

D: Apoptosis-inducing factor 1, mitochondrial

G: Apoptosis-inducing factor 1, mitochondrial

J: Apoptosis-inducing factor 1, mitochondrial

M: Mitochondrial intermembrane space import and assembly protein 40

N: Mitochondrial intermembrane space import and assembly protein 40

O: Mitochondrial intermembrane space import and assembly protein 40

P: Mitochondrial intermembrane space import and assembly protein 40

hetero molecules

247 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Apoptosis-inducing factor 1, mitochondrial

M: Mitochondrial intermembrane space import and assembly protein 40

hetero molecules

defined by author&software
Evidence: cross-linking
61.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Apoptosis-inducing factor 1, mitochondrial

O: Mitochondrial intermembrane space import and assembly protein 40

hetero molecules

defined by author&software
Evidence: cross-linking
61.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Apoptosis-inducing factor 1, mitochondrial

N: Mitochondrial intermembrane space import and assembly protein 40

hetero molecules

defined by author&software
Evidence: cross-linking
61.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Apoptosis-inducing factor 1, mitochondrial

P: Mitochondrial intermembrane space import and assembly protein 40

hetero molecules

defined by author&software
Evidence: cross-linking
61.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.087, 115.619, 192.727
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:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	125 - 612
2	1	1	A	125 - 612
3	2	2	A	127 - 611
4	2	2	A	127 - 611
5	3	3	A	128 - 610
6	3	3	A	128 - 610
7	4	4	A	127 - 612
8	4	4	A	127 - 612
9	5	5	A	128 - 610
10	5	5	A	128 - 610
11	6	6	A	128 - 610
12	6	6	A	128 - 610
13	7	7	A	2 - 18
14	7	7	A	2 - 18
15	8	8	A	3 - 18
16	8	8	A	3 - 18
17	9	9	A	3 - 19
18	9	9	A	3 - 19

NCS ensembles :

ID	Details
1	Global NCS restraints between domains: 1 2
2	Global NCS restraints between domains: 3 4
3	Global NCS restraints between domains: 5 6
4	Global NCS restraints between domains: 7 8
5	Global NCS restraints between domains: 9 10
6	Global NCS restraints between domains: 11 12
7	Global NCS restraints between domains: 13 14
8	Global NCS restraints between domains: 15 16
9	Global NCS restraints between domains: 17 18

#1: Protein	Apoptosis-inducing factor 1, mitochondrial / Programmed cell death protein 8 Mass: 57149.871 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aifm1, Aif, Pdcd8 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Z0X1, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Protein/peptide	Mitochondrial intermembrane space import and assembly protein 40 Mass: 3162.486 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VEA4
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H₂O
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: 3.04 Å³/Da / Density % sol: 59.56 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 6k, 100 mM Tris-HCl pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96546 Å / Relative weight: 1
Reflection	Resolution: 3.206→99.146 Å / Num. obs: 24919 / % possible obs: 93.6 % / Redundancy: 13.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.303 / R_pim(I) all: 0.086 / R_rim(I) all: 0.315 / Net I/σ(I): 7.6
Reflection shell	Resolution: 3.206→3.483 Å / Redundancy: 13.6 % / R_merge(I) obs: 1.878 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1247 / CC_1/2: 0.656 / R_pim(I) all: 0.525 / R_rim(I) all: 1.951 / % possible all: 64.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.206→99.146 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.869 / SU B: 77.311 / SU ML: 0.598 / Cross valid method: THROUGHOUT / ESU R Free: 0.863
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2844	1236	4.96 %	RANDOM
R_work	0.2325	23683	-	-
all	0.235	-	-	-
obs	-	24919	60.652 %	-

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: 76.592 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.107 Å²	0 Å²	0 Å²
2-	-	-2.913 Å²	0 Å²
3-	-	-	-0.194 Å²

Refinement step

Cycle: LAST / Resolution: 3.206→99.146 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14227	0	388	86	14701

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	14932
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14311
X-RAY DIFFRACTION	r_angle_refined_deg	1.204	1.655	20228
X-RAY DIFFRACTION	r_angle_other_deg	0.67	1.582	32917
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.535	5	1819
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.763	5	123
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.965	12.5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.478	10	2538
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.143	10	643
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	2230
X-RAY DIFFRACTION	r_chiral_restr_other	1.537	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	17566
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3434
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	3018
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.228	0.2	14487
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	7227
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	8197
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	339
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.023	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.238	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.288	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.607	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0	2	7315
X-RAY DIFFRACTION	r_mcbond_other	0	2	7315
X-RAY DIFFRACTION	r_mcangle_it	0	3.592	9121
X-RAY DIFFRACTION	r_mcangle_other	0	3.592	9122
X-RAY DIFFRACTION	r_scbond_it	0	2.232	7617
X-RAY DIFFRACTION	r_scbond_other	0	2.232	7618
X-RAY DIFFRACTION	r_scangle_it	0	4.133	11107
X-RAY DIFFRACTION	r_scangle_other	0	4.133	11108
X-RAY DIFFRACTION	r_lrange_it	4.461	21.186	16289
X-RAY DIFFRACTION	r_lrange_other	4.461	21.18	16287

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.21856	0.08661
1	2	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.21856	0.08661
2	3	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.22047	0.08661
2	4	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.22047	0.08661
3	5	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.18758	0.08661
3	6	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.18758	0.08661
4	7	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.20329	0.08661
4	8	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.20329	0.08661
5	9	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.11847	0.08661
5	10	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.11847	0.08661
6	11	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.11696	0.08661
6	12	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.11696	0.08661
7	13	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.44928	0.07071
7	14	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.44928	0.07071
8	15	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.25785	0.07071
8	16	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.25785	0.07071
9	17	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.3255	0.07071
9	18	A	X-RAY DIFFRACTION	tight positional; tight thermal	0.3255	0.07071

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
3.206-3.289	0.363	8	0.324	157	0.326	2954	0.913	0.907	5.5856	0.323
3.289-3.379	0.404	12	0.313	382	0.316	2938	0.919	0.92	13.4105	0.305
3.379-3.477	0.235	27	0.319	614	0.316	2844	0.976	0.925	22.5387	0.313
3.477-3.584	0.362	42	0.295	854	0.298	2751	0.882	0.936	32.57	0.289
3.584-3.701	0.376	54	0.271	1016	0.276	2695	0.911	0.947	39.7032	0.261
3.701-3.831	0.339	73	0.282	1145	0.285	2573	0.916	0.941	47.3377	0.269
3.831-3.975	0.331	58	0.282	1349	0.284	2519	0.928	0.942	55.8555	0.261
3.975-4.138	0.296	71	0.258	1477	0.26	2417	0.938	0.954	64.0463	0.234
4.138-4.321	0.273	84	0.237	1580	0.239	2316	0.954	0.963	71.848	0.208
4.321-4.532	0.262	89	0.226	1641	0.228	2222	0.962	0.967	77.8578	0.198
4.532-4.776	0.273	78	0.212	1711	0.214	2126	0.948	0.969	84.1486	0.186
4.776-5.065	0.244	105	0.212	1688	0.214	1997	0.956	0.971	89.7847	0.185
5.065-5.414	0.311	95	0.224	1684	0.228	1904	0.936	0.966	93.4349	0.197
5.414-5.846	0.295	80	0.254	1689	0.256	1770	0.957	0.958	99.9435	0.221
5.846-6.402	0.32	72	0.242	1579	0.246	1651	0.928	0.965	100	0.221
6.402-7.154	0.38	77	0.252	1405	0.259	1482	0.93	0.963	100	0.232
7.154-8.254	0.268	69	0.215	1260	0.217	1329	0.943	0.971	100	0.201
8.254-10.091	0.211	71	0.169	1071	0.172	1142	0.974	0.983	100	0.175
10.091-14.197	0.252	37	0.179	865	0.182	902	0.957	0.982	100	0.193
14.197-99.146	0.27	34	0.299	516	0.297	551	0.934	0.933	99.8185	0.313

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	1.1638	-0.9226	0.9236	5.4506	0.3303	3.678	-0.0813	-0.1841	0.1448	0.1937	0.0831	-0.1811	-0.2217	-0.0091	-0.0018	0.2185	-0.0705	-0.0455	0.0641	-0.013	0.0311	1.6104	23.59	44.8759
2	2.0549	0.047	-0.0642	3.1283	-0.3818	4.8605	0.2543	0.824	0.0484	-0.2606	0.0313	-0.4256	0.3338	0.5732	-0.2856	0.2186	0.1237	-0.004	0.4644	-0.0755	0.1378	2.9143	2.4699	3.4652
3	1.9594	-0.322	0.5807	2.81	-0.2613	3.5894	0.095	-0.7617	0.235	-0.0322	0.0268	-0.2454	-0.2483	-0.4811	-0.1218	0.1008	-0.0189	-0.1116	0.9165	-0.0096	0.3302	-52.5993	18.308	47.6283
4	3.5927	0.5211	0.8515	3.2945	1.4668	2.9073	0.3492	0.9613	-1.559	-0.4253	0.1146	-0.5884	0.3296	0.0647	-0.4638	0.3952	0.1638	-0.1839	1.0183	-0.3076	1.0467	-53.1688	-3.8933	6.8682
5	30.3723	6.7554	-18.1366	2.7612	-2.9366	11.8708	-0.1631	-0.2202	0.1479	-0.206	-0.2818	0.7942	0.0202	-0.2058	0.4449	0.5733	0.1868	-0.177	0.42	0.0849	0.6666	-24.6924	37.6387	36.2256
6	11.0767	6.8274	3.9084	5.2605	1.4344	2.2899	0.1315	-0.2848	-0.1506	0.1289	-0.0733	-0.1054	-0.0278	-0.1246	-0.0581	0.4803	-0.0243	0.0654	0.7822	-0.0702	0.7942	-26.2969	3.2066	56.2252
7	10.5905	-3.7566	-6.2263	1.3476	2.22	3.6856	-0.5688	0.1584	-0.4861	0.2356	0.1172	0.1677	0.34	0.0132	0.4515	0.8699	0.1371	-0.0195	1.3862	-0.0964	1.2661	29.0581	18.4911	-4.1677
8	0.3219	1.6356	0.4873	8.4223	2.4935	0.7425	-0.0124	0.0528	-0.0383	0.0142	0.011	0.0283	0.0035	0.0718	0.0014	0.4941	-0.0394	-0.006	1.1099	-0.1135	0.9329	-76.3642	-18.3131	18.7114

Refinement TLS group

Selection: ALL

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