PDB-8iql: Structural basis of the specificity and interaction mechanism of ...

ID or keywords:

Entry

Database: PDB / ID: 8iql

Title

Structural basis of the specificity and interaction mechanism of Bmf binding to pro-survival proteins

Components

Apoptosis regulator Bcl-2
Bcl-2-modifying factor

Keywords

APOPTOSIS / Complex

Function / homology

Function and homology information

Activation of BMF and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / myosin complex / anoikis / positive regulation of release of cytochrome c from mitochondria / negative regulation of autophagy / positive regulation of protein-containing complex assembly / cellular response to UV / mitochondrial outer membrane / positive regulation of apoptotic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9577 Å

Authors

Wang, H. / Guo, M. / Wei, H. / Chen, Y.

Funding support

China, 5items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	81570537	China
National Natural Science Foundation of China (NSFC)	81974074	China
National Natural Science Foundation of China (NSFC)	82172654	China
National Natural Science Foundation of China (NSFC)	82273496	China
National Natural Science Foundation of China (NSFC)	31900880	China

Citation

Journal: Comput Struct Biotechnol J / Year: 2023
Title: Structural basis of the specificity and interaction mechanism of Bmf binding to pro-survival Bcl-2 family proteins.
Authors: Wang, H. / Guo, M. / Wei, H. / Chen, Y.

History

Deposition	Mar 16, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 23, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8iql.cif.gz	144.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8iql.ent.gz	114.1 KB	Display	PDB format
PDBx/mmJSON format	8iql.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8iql_validation.pdf.gz	446.2 KB	Display	wwPDB validaton report
Full document	8iql_full_validation.pdf.gz	448.6 KB	Display
Data in XML	8iql_validation.xml.gz	12.6 KB	Display
Data in CIF	8iql_validation.cif.gz	16 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/8iql ftp://data.pdbj.org/pub/pdb/validation_reports/iq/8iql	HTTPS FTP

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Related structure data

Related structure data	8iqkC 8iqmC 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

Deposited unit

C: Apoptosis regulator Bcl-2

D: Bcl-2-modifying factor

A: Apoptosis regulator Bcl-2

B: Bcl-2-modifying factor

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

1

C: Apoptosis regulator Bcl-2

D: Bcl-2-modifying factor

defined by author&software
Evidence: isothermal titration calorimetry
22.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Apoptosis regulator Bcl-2

B: Bcl-2-modifying factor

defined by author&software
22.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.743, 122.743, 86.431
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Apoptosis regulator Bcl-2 Mass: 19357.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide	Bcl-2-modifying factor Mass: 3003.440 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMF / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LC9

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.2 Å³/Da / Density % sol: 70.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M potassium thiocyanate, polyethylene glycol monomethyl ether 2,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 30, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.9577→32.7868 Å / Num. obs: 30365 / % possible obs: 99.88 % / Redundancy: 10.7 % / CC_1/2: 0.997 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.9577→3.063 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1605 / CC_1/2: 0.78

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
xia2		data reduction
SCALEPACK		data scaling
PHENIX	1.9_1692	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9577→32.7868 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2262	3041	10.01 %
R_work	0.1888	-	-
obs	0.1925	30365	99.72 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.9577→32.7868 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2541	0	0	0	2541

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2641
X-RAY DIFFRACTION	f_angle_d	0.57	3583
X-RAY DIFFRACTION	f_dihedral_angle_d	14.053	909
X-RAY DIFFRACTION	f_chiral_restr	0.022	379
X-RAY DIFFRACTION	f_plane_restr	0.002	460

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.9577-3.0039	0.3587	150	0.3122	1277	X-RAY DIFFRACTION	100
3.0039-3.0531	0.3658	132	0.3223	1234	X-RAY DIFFRACTION	100
3.0531-3.1057	0.3705	138	0.3115	1233	X-RAY DIFFRACTION	100
3.1057-3.1622	0.3074	144	0.3059	1242	X-RAY DIFFRACTION	100
3.1622-3.2229	0.3156	134	0.3063	1276	X-RAY DIFFRACTION	100
3.2229-3.2887	0.3649	143	0.2643	1201	X-RAY DIFFRACTION	100
3.2887-3.3601	0.282	140	0.2561	1228	X-RAY DIFFRACTION	100
3.3601-3.4382	0.3796	138	0.2521	1251	X-RAY DIFFRACTION	100
3.4382-3.5241	0.234	140	0.2402	1238	X-RAY DIFFRACTION	100
3.5241-3.6192	0.2638	140	0.2209	1252	X-RAY DIFFRACTION	100
3.6192-3.7256	0.2322	142	0.2329	1259	X-RAY DIFFRACTION	100
3.7256-3.8457	0.234	138	0.194	1241	X-RAY DIFFRACTION	100
3.8457-3.9829	0.1893	136	0.1983	1223	X-RAY DIFFRACTION	100
3.9829-4.1421	0.2015	136	0.1708	1246	X-RAY DIFFRACTION	100
4.1421-4.3302	0.1764	134	0.1603	1273	X-RAY DIFFRACTION	100
4.3302-4.5579	0.1902	142	0.1607	1241	X-RAY DIFFRACTION	100
4.5579-4.8426	0.1997	134	0.1445	1241	X-RAY DIFFRACTION	100
4.8426-5.2152	0.1848	135	0.1461	1233	X-RAY DIFFRACTION	100
5.2152-5.7375	0.2067	146	0.1709	1256	X-RAY DIFFRACTION	100
5.7375-6.5619	0.2315	135	0.1866	1233	X-RAY DIFFRACTION	100
6.5619-8.2455	0.2456	136	0.1829	1245	X-RAY DIFFRACTION	100
8.2455-32.7868	0.1749	128	0.1394	1201	X-RAY DIFFRACTION	96

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	0.474	0.3916	0.1422	0.3168	0.181	0.5079	0.447	-0.5639	0.3421	-0.0688	-0.5167	0.8832	0.1129	-0.3731	0.0015	0.5366	-0.0294	0.0496	0.7222	-0.0029	0.7205	41.5344	175.8907	20.0076
2	0.2865	-0.1518	0.0698	0.0318	-0.102	0.1869	-0.1761	-0.427	-0.542	-0.084	0.4436	0.1987	-0.2341	-0.4723	0.0002	0.5692	-0.1109	0.0345	0.684	-0.0086	0.6483	45.5365	163.5817	16.7434
3	0.0278	0.0537	0.1004	0.2318	0.1556	0.2017	0.0674	-0.2641	0.5551	-0.1228	0.3631	-0.1497	0.0938	0.7745	0	0.466	-0.0807	-0.0208	0.733	-0.064	0.5997	59.501	171.1954	27.5978
4	2.7549	-0.4573	-0.4318	0.8034	0.2814	1.0741	0.1883	0.1541	0.1472	-0.1893	-0.1985	0.0377	-0.2664	0.1966	-0.0006	0.4715	-0.0403	0.0343	0.592	-0.0255	0.5685	52.1831	173.6994	16.3177
5	0.3713	0.0636	0.2303	0.014	0.0263	0.1213	0.0768	1.3357	-0.7182	-0.1285	0.2524	-0.2811	0.2165	0.335	0.0115	0.7543	0.0378	0.0556	0.7195	-0.0268	0.7821	56.6501	160.0289	13.5727
6	0.2646	0.1581	0.2238	0.1276	-0.0342	0.3402	-0.5061	1.7508	0.1697	-0.3062	0.3178	0.0487	0.1631	0.5791	-0.0014	0.8687	-0.3088	-0.015	1.0353	-0.1506	0.7634	29.4792	151.3145	5.7482
7	1.3559	0.7583	0.465	0.7317	0.4034	0.1863	-0.5164	0.3205	-0.1901	-0.3515	0.4266	0.1707	-0.0754	0.2993	0.0003	0.6871	-0.3156	-0.0294	0.9248	0.0311	0.7262	28.914	159.8984	8.661
8	0.199	-0.0924	-0.4701	0.7582	0.0875	1.0541	-0.4334	-0.1711	0.1637	-0.1498	0.6075	0.2354	-0.5359	-0.2337	-0.0002	0.5371	-0.1427	0.0075	0.9041	0.0861	0.6762	20.8414	159.182	12.973
9	0.5187	-0.1187	0.1347	1.6208	-1.2654	0.854	-0.3075	0.8044	-0.1558	-0.0812	0.1045	-0.0079	-0.0697	0.3618	0.0002	0.6523	-0.2414	-0.019	0.9255	-0.0423	0.5924	20.2297	152.396	7.914
10	0.0181	0.0248	0.0153	0.147	-0.1684	0.2159	0.0733	0.371	0.2959	-0.1202	0.6799	0.4277	0.2523	-0.3767	-0.0026	0.6842	-0.1883	-0.0798	1.0915	0.1874	0.9493	17.7942	168.9705	6.3923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 9 through 90 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 91 through 116 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 117 through 137 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 138 through 204 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 31 through 49 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 9 through 26 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 27 through 125 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 126 through 163 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 164 through 204 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 31 through 49 )

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