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

ID or keywords:

Entry

Database: PDB / ID: 8iqk

Title

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

Components

Bcl-2-like protein 1
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 / anoikis / myosin complex / 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: 2.879 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
Revision 1.1	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8iqk.cif.gz	270.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8iqk.ent.gz	219.7 KB	Display	PDB format
PDBx/mmJSON format	8iqk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8iqk_validation.pdf.gz	473 KB	Display	wwPDB validaton report
Full document	8iqk_full_validation.pdf.gz	475.2 KB	Display
Data in XML	8iqk_validation.xml.gz	22.7 KB	Display
Data in CIF	8iqk_validation.cif.gz	30.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/8iqk ftp://data.pdbj.org/pub/pdb/validation_reports/iq/8iqk	HTTPS FTP

-
Related structure data

Related structure data	8iqlC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bcl-2-like protein 1

B: Bcl-2-modifying factor

C: Bcl-2-like protein 1

D: Bcl-2-modifying factor

E: Bcl-2-like protein 1

F: Bcl-2-modifying factor

G: Bcl-2-like protein 1

H: Bcl-2-modifying factor

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

1

A: Bcl-2-like protein 1

B: Bcl-2-modifying factor

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

2

C: Bcl-2-like protein 1

D: Bcl-2-modifying factor

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

3

E: Bcl-2-like protein 1

F: Bcl-2-modifying factor

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

4

G: Bcl-2-like protein 1

H: Bcl-2-modifying factor

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

Unit cell

Length a, b, c (Å)	102.524, 61.668, 102.528
Angle α, β, γ (deg.)	90.00, 90.19, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein	Bcl-2-like protein 1 Mass: 19515.490 Da / Num. of mol.: 4 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.: 4 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
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65.82 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium chloride, 0.1 M sodium acetate: acetic acid, pH 4.5, 1.26 M ammonium sulfate

-
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: Nov 9, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.879→39.4252 Å / Num. obs: 27310 / % possible obs: 92.98 % / Redundancy: 6.3 % / CC_1/2: 0.991 / Net I/σ(I): 8.92
Reflection shell	Resolution: 2.879→2.982 Å / Num. unique obs: 2523 / CC_1/2: 0.655

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.879→39.4252 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.255	1977	7.24 %
R_work	0.2264	-	-
obs	0.2285	27310	92.62 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.879→39.4252 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5108	0	0	0	5108

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5238
X-RAY DIFFRACTION	f_angle_d	0.679	7104
X-RAY DIFFRACTION	f_dihedral_angle_d	13.882	1754
X-RAY DIFFRACTION	f_chiral_restr	0.026	771
X-RAY DIFFRACTION	f_plane_restr	0.003	914

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 (%)
2.879-2.9509	0.4116	124	0.2988	1528	X-RAY DIFFRACTION	79
2.9509-3.0306	0.3482	149	0.2893	1941	X-RAY DIFFRACTION	100
3.0306-3.1198	0.3533	157	0.2595	1922	X-RAY DIFFRACTION	100
3.1198-3.2204	0.2647	152	0.2829	1962	X-RAY DIFFRACTION	100
3.2204-3.3355	0.2768	148	0.2678	1950	X-RAY DIFFRACTION	100
3.3355-3.469	0.3182	148	0.2516	1907	X-RAY DIFFRACTION	100
3.469-3.6267	0.2752	140	0.2428	1812	X-RAY DIFFRACTION	93
3.6267-3.8178	0.2675	75	0.3052	987	X-RAY DIFFRACTION	51
3.8178-4.0568	0.2911	111	0.2186	1460	X-RAY DIFFRACTION	76
4.0568-4.3696	0.201	150	0.1927	1946	X-RAY DIFFRACTION	100
4.3696-4.8087	0.2386	153	0.1884	1965	X-RAY DIFFRACTION	100
4.8087-5.5029	0.2552	156	0.2001	1960	X-RAY DIFFRACTION	100
5.5029-6.9269	0.2751	150	0.2479	1985	X-RAY DIFFRACTION	100
6.9269-39.4252	0.186	164	0.1939	2008	X-RAY DIFFRACTION	99

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	0.893	0.6155	-0.3732	0.6049	-0.534	0.5605	0.0319	-0.3665	-0.0536	0.1422	0.0344	0.0323	0.194	-0.0871	-0	0.4478	0.0554	-0.0309	0.3901	0.04	0.4011	6.7295	12.9221	22.8495
2	0.1466	0.0883	0.0985	0	0.0606	0.0608	-0.2735	0.2048	0.516	-0.0213	0.102	0.279	-2.0212	-0.0033	0.0009	0.793	-0.0172	0.0366	0.691	-0.0845	0.7134	10.6206	29.0123	15.4111
3	0.6608	-0.5125	-1.0855	1.4469	-0.2196	2.1387	0.1317	0.0834	-0.1065	-0.084	-0.0025	-0.0879	0.1386	0.6546	-0	0.336	0.0581	-0.0457	0.3098	0.0184	0.2967	15.5348	18.7048	16.7629
4	1.6997	0.0889	-1.8017	0.2962	-0.0151	3.9779	0.7458	-0.8098	-0.5912	0.9213	0.0982	-0.6581	-0.9683	1.7588	0.2112	0.9304	0.1507	-0.1852	0.8804	0.2307	0.6339	20.6378	8.7746	30.4089
5	0.454	-0.2067	-0.2494	0.3789	-0.313	2.6902	-0.7864	-0.8119	0.2039	0.6138	-0.5271	-0.9618	-1.3446	0.1538	-0.6391	0.4542	-0.0918	-0.0377	0.831	-0.0801	0.5003	19.1855	27.5775	26.0209
6	0.6349	-0.4909	0.3382	0.3639	0.0139	1.2453	-0.0266	0.0712	-0.146	0.0644	0.1014	0.0691	-0.0912	0.3026	-0.0002	0.4692	0.0511	0.0595	0.4009	-0.0416	0.4515	23.0033	12.971	-6.7469
7	0.0364	0.0052	-0.0278	-0.0039	-0.0376	0.0259	0.5271	-0.5668	0.8517	0.3639	-0.1103	0.3898	-0.4573	-0.3029	0.0016	0.6832	-0.0553	0.0017	0.4643	0.0264	0.7537	17.9862	29.8825	-9.954
8	1.9585	0.2939	0.6149	1.7432	0.2054	0.2522	-0.0537	0.7135	-0.0916	-0.0873	0.1546	0.1445	0.1888	-0.0793	0.0002	0.3529	0.0185	-0.0002	0.3769	-0.0311	0.3853	16.505	18.8648	-15.8561
9	4.5919	0.2308	2.5593	0.8435	-0.4857	1.9315	-0.4249	1.2611	1.1912	-0.2737	-0.0598	-0.8498	0.8608	1.2454	-0.211	0.6164	0.2432	0.1511	0.7809	-0.2009	0.936	31.3109	8.378	-20.1326
10	0.1218	-0.1245	0.1506	0.6466	0.103	0.3636	0.6219	0.6623	1.3273	-0.4351	-0.0699	-1.0472	-0.4355	0.3343	0.015	0.5938	-0.0184	0.0785	0.7465	0.1165	0.5559	22.0728	29.948	-20.1848
11	3.0282	0.0402	-0.992	0.2259	0.0385	2.1979	0.7697	0.4257	0.5969	-0.8873	-0.1553	-1.2493	-0.5696	0.7024	0.2109	0.7098	0.0742	-0.0041	1.2939	0.1435	0.7282	36.1838	21.8707	-17.1102
12	0.896	-0.3405	0.0479	0.0798	-0.1696	1.1963	-0.0123	-0.1116	0.3299	0.062	-0.0702	-0.0887	0.0855	-0.5982	-0.01	0.3741	0.0378	-0.041	0.3227	0.033	0.3812	28.1528	49.1254	44.4408
13	0.0303	0.0551	0.0556	0.0299	0.0995	0.1252	0.3047	-0.4954	-1.6336	0.4411	-0.0907	-0.2787	0.4372	0.304	0.0001	0.7009	-0.1287	0.1071	0.5061	0.0309	0.6763	35.6926	33.1355	40.5923
14	1.8327	-0.1505	-0.9676	1.4112	-0.2358	0.5261	-0.0985	0.5472	0.1721	-0.0477	0.0974	-0.0603	-0.1902	-0.034	0.0002	0.2609	-0.0106	-0.0356	0.2891	0.0927	0.3268	34.3509	43.4284	35.6686
15	1.7645	0.7117	0.1066	0.5067	0.2705	0.354	-0.415	0.8868	-0.825	-1.037	0.032	1.6172	-0.3634	-0.6074	0.0349	0.8245	0.1371	-0.2072	0.8151	0.1845	1.0147	20.7719	53.4471	30.6127
16	0.0916	-0.0904	-0.1915	0.2812	0.1428	0.4094	0.4484	0.9377	-0.9728	-0.4828	-0.2533	0.7677	0.424	-0.4388	0.0413	0.5757	-0.1176	-0.0517	0.7154	-0.1212	0.5198	29.267	32.1581	30.9034
17	0.1136	0.0226	-0.9192	3.2992	-1.8969	8.5399	0.9933	0.3517	0.0384	-0.4065	0.1154	0.4085	0.5744	-0.7021	1.849	0.5835	0.1736	0.0942	2.1252	0.1844	0.4636	15.0009	40.2388	34.0161
18	1.5109	0.0345	-0.1519	0.8665	-0.5526	0.3313	0.0213	0.447	0.1201	0.2849	0.1666	0.075	-0.0831	0.0373	0.0004	0.4696	-0.0464	0.0418	0.4126	0.0539	0.5054	57.9404	49.2337	28.3266
19	0.005	0.0056	-0.0756	-0.0323	-0.0151	0.1667	-0.4355	-0.4345	-1.1536	0.2572	-0.7688	0.9686	1.1044	-0.3828	-0.0083	0.8316	-0.0843	-0.0402	0.4987	-0.0416	0.6978	61.0866	32.1903	33.2557
20	0.4857	0.2632	0.9696	1.4481	-0.1521	1.8727	0.0305	-0.1284	0.0534	0.1554	0.114	-0.0439	-0.1864	0.6146	0	0.3271	-0.0533	0.0125	0.3666	0.013	0.3055	66.7164	43.2028	34.933
21	0.7282	-0.4297	0.5745	0.3746	-0.0889	1.6011	0.4542	0.5885	0.7977	-1.3621	0.0446	-0.3714	1.3226	0.996	0.0584	0.8765	-0.1421	0.154	0.805	0.1718	0.68	71.7774	53.3282	20.7327
22	0.3538	-0.0463	-0.04	0.2913	0.0764	0.023	-0.3018	0.3164	-0.4051	-0.7793	-0.1296	-0.169	1.0777	0.8183	0.0016	0.587	0.0913	0.0506	0.6951	-0.0937	0.6162	71.1599	32.2588	29.0159
23	4.3876	1.213	-1.3527	2.1149	-0.6598	0.469	-0.6726	0.911	-1.0853	-0.8074	-0.5303	-0.4219	0.2837	0.0706	-0.2997	0.3672	0.0113	-0.2299	1.8213	0.0791	0.6041	68.3729	40.2432	15.0868

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 104 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 105 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 176 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 177 through 196 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 127 through 147 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1 through 104 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 105 through 115 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 116 through 177 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 178 through 196 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 127 through 141 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 142 through 147 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 1 through 104 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 105 through 118 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 119 through 176 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 177 through 196 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 127 through 141 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 142 through 147 )
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 1 through 104 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 105 through 115 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 116 through 176 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 177 through 196 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 127 through 141 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 142 through 147 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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