PDB-7x4w: Crystal structure of Keap1 BTB domain in complex with dimethyl fu...

ID or keywords:

Entry

Database: PDB / ID: 7x4w

Title

Crystal structure of Keap1 BTB domain in complex with dimethyl fumarate (DMF)

Components

Kelch-like ECH-associated protein 1

Keywords

SIGNALING PROTEIN / KEAP1 / BTB domain

Function / homology

Function and homology information

regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.209 Å

Authors

Qu, L.Z.

Funding support

China, 1items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Characterization of the modification of Kelch-like ECH-associated protein 1 by different fumarates.
Authors: Qu, L. / Guo, M. / Zhang, H. / Chen, X. / Wei, H. / Jiang, L. / Li, J. / Chen, Z. / Dai, S. / Chen, Y.

History

Deposition	Mar 3, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author 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
Revision 1.2	Nov 29, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x4w.cif.gz	298.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7x4w.ent.gz	243.3 KB	Display	PDB format
PDBx/mmJSON format	7x4w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x4w_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	7x4w_full_validation.pdf.gz	1 MB	Display
Data in XML	7x4w_validation.xml.gz	27.4 KB	Display
Data in CIF	7x4w_validation.cif.gz	36.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/7x4w ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x4w	HTTPS FTP

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Related structure data

Related structure data	7x4xC 4cxiS S: Starting model for refinement 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	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1)

Deposited unit

A: Kelch-like ECH-associated protein 1

C: Kelch-like ECH-associated protein 1

D: Kelch-like ECH-associated protein 1

E: Kelch-like ECH-associated protein 1

F: Kelch-like ECH-associated protein 1

B: Kelch-like ECH-associated protein 1

hetero molecules

93.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kelch-like ECH-associated protein 1

D: Kelch-like ECH-associated protein 1

hetero molecules

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

2

C: Kelch-like ECH-associated protein 1

B: Kelch-like ECH-associated protein 1

hetero molecules

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

3

E: Kelch-like ECH-associated protein 1

F: Kelch-like ECH-associated protein 1

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

Unit cell

Length a, b, c (Å)	84.538, 99.105, 143.136
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19 Mass: 15509.844 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14145
#2: Chemical	ChemComp-9HB / Dimethyl fumarate Mass: 146.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₀O₄ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	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: 3.22 Å³/Da / Density % sol: 61.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M lithium acetate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.58 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 25, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.58 Å / Relative weight: 1
Reflection	Resolution: 3.2→46.826 Å / Num. obs: 19199 / % possible obs: 94.6 % / Redundancy: 8.4 % / CC_1/2: 1 / Net I/σ(I): 6.8
Reflection shell	Resolution: 3.2→3.3 Å / Num. unique obs: 1811 / CC_1/2: 0.5

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4CXI

4cxi

Resolution: 3.209→46.826 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2979	1921	10.01 %
R_work	0.2375	17278	-
obs	0.2437	19199	94.67 %

Solvent computation

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

Displacement parameters

B_iso max: 137.22 Å² / B_iso mean: 63.4388 Å² / B_iso min: 20.74 Å²

Refinement step

Cycle: final / Resolution: 3.209→46.826 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5639	0	30	0	5669
B_iso mean	-	-	91.25	-	-
Num. residues	-	-	-	-	750

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5766
X-RAY DIFFRACTION	f_angle_d	0.417	7796
X-RAY DIFFRACTION	f_chiral_restr	0.04	928
X-RAY DIFFRACTION	f_plane_restr	0.003	987
X-RAY DIFFRACTION	f_dihedral_angle_d	13.851	3441

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.2094-3.2897	0.4149	125	0.3349	1124	89
3.2897-3.3786	0.3739	134	0.3074	1207	94
3.3786-3.478	0.4055	132	0.3477	1212	95
3.478-3.5902	0.3635	134	0.2959	1205	93
3.5902-3.7185	0.3797	132	0.3007	1186	92
3.7185-3.8673	0.3653	135	0.297	1210	93
3.8673-4.0432	0.37	132	0.2768	1179	92
4.0432-4.2562	0.2785	133	0.2103	1194	92
4.2562-4.5227	0.2864	133	0.2035	1201	93
4.5227-4.8716	0.2509	137	0.1828	1227	95
4.8716-5.3612	0.21	143	0.2017	1289	98
5.3612-6.1355	0.3128	147	0.2321	1321	100
6.1355-7.7244	0.2702	148	0.2378	1340	100
7.7244-46.826	0.2362	156	0.1849	1383	98

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	0.2631	0.0967	0.5575	-0.0606	0.1208	0.9784	-0.0435	0.1126	-0.1925	-0.0383	0.0791	-0.1272	0.0595	-0.0078	-0.0006	0.2439	0.006	-0.0166	0.2431	0.0371	0.3151	79.634	109.756	50.104
2	0.9801	0.373	0.5624	0.1447	0.1614	0.8711	0.3795	0.0317	-0.1731	-0.0281	0.3018	-0.1483	-0.5441	0.1436	0.5828	0.9039	0.3739	0.1807	0.7678	0.1652	0.0748	90.94	117.607	41.311
3	0.1061	-0.2183	0.0368	0.2837	-0.0377	0.0758	0.131	0.1163	0.0526	-0.137	0.0561	0.1128	-0.1847	-0.2044	0.0393	0.3084	0.0117	0.1019	0.2885	0.0394	0.1735	82.079	117.545	57.214
4	0.0547	0.1855	0.077	0.4389	0.0341	1.7833	-0.0373	0.1664	-0.0946	-0.0037	0.3186	0.0646	-0.8612	0.4871	0.1645	0.2975	-0.0036	-0.0482	0.1944	0.0195	0.3251	70.8	122.543	60.283
5	1.0284	-0.2838	-0.7704	0.5328	0.4483	0.7986	0.0917	0.0588	0.0036	-0.0557	-0.2328	0.3168	-0.0877	-0.1445	-0.1485	0.3696	0.0609	-0.0414	0.2324	0.0109	0.3554	79.082	115.462	18.594
6	0.6268	-0.3119	0.244	0.1927	-0.0796	0.0484	0.3614	0.2842	0.1944	-0.0288	-0.2612	-0.0878	0.1095	0.3146	0.0298	0.3748	-0.0667	0.0293	0.2866	-0.0436	0.2824	99.487	120.933	14.784
7	0.3613	-0.2801	0.0998	0.2717	-0.2161	0.2651	-0.0286	0.0842	0.3504	-0.2643	-0.0456	0.061	-0.1033	0.2095	-0.0587	-0.1044	0.909	-0.8946	-0.1113	0.8436	-0.5638	99.749	126.112	3.791
8	1.0102	-0.2984	0.8523	0.0835	-0.2663	0.7346	0.0956	0.3994	0.1418	-0.2036	-0.133	-0.5504	-0.0661	0.5218	-0.0353	0.4077	-0.0475	-0.0257	0.1821	0.046	0.6511	106.683	123.754	16.289
9	0.0094	0.005	-0.0162	0.0966	-0.2239	0.4532	-0.3716	-0.3748	0.0817	-0.2544	0.6804	-0.1318	0.0124	-0.8693	0.0288	0.3208	-0.0201	0.0001	0.3995	-0.0607	0.453	97.914	118.233	24.207
10	0.2419	0.1559	0.2531	0.1119	0.2105	0.421	-0.0272	-0.477	0.4402	0.0147	0.1532	-0.1071	-0.0887	0.0969	0.2566	0.3607	0.0342	0.2721	0.6327	-0.4302	0.4026	98.606	118.898	34.251
11	0.4164	0.136	0.3674	0.1516	0.1009	0.3055	0.2277	0.1822	-0.4918	-0.1188	0.1294	-0.1768	0.1731	0.154	0.2512	0.6339	0.2181	0.1775	-0.5696	-0.071	0.4448	100.981	128.249	28.3
12	0.0308	-0.0049	-0.0246	-0.011	0.0134	0.0117	0.0196	0.3012	-0.2972	-0.1712	-0.0232	0.0128	0.2113	-0.0888	-0.0003	0.3966	0.0249	0.0106	0.2521	0.0769	0.4441	94.93	128.666	36.102
13	0.3981	0.2221	-0.0762	0.1839	-0.0369	0.1673	0.0728	0.0794	-0.2685	0.0051	0.075	0.0522	-0.3207	-0.1719	0.0062	0.2932	0.1066	-0.0626	0.2958	0.0147	0.2369	81.951	122.904	10.468
14	0.8118	-0.4451	0.0838	0.553	-0.2626	0.2273	-0.0971	-0.7117	-0.2722	-0.1251	0.2369	0.256	-0.196	0.4398	0.0193	0.3746	-0.0305	-0.0539	0.4419	-0.0248	0.2568	79.034	115.903	4.493
15	0.0873	-0.1034	-0.1243	0.0488	0.0214	0.0018	-0.2645	0.4245	0.4388	0.2365	-0.1058	-0.2065	-0.1991	-0.2956	-0.0003	0.3969	-0.1122	-0.0719	0.6023	-0.0346	0.4369	64.01	113.392	10.905
16	0.674	0.3163	0.3485	0.496	-0.3046	0.6496	0.0605	-0.1173	-0.086	-0.0484	0.0316	0.0051	-0.0056	0.1197	0	0.3193	-0.0085	0.0396	0.2356	-0.0149	0.3562	79.19	103.639	39.074
17	0.0423	0.2197	0.1224	0.0875	-0.018	0.0619	0.2737	0.1455	0.0189	-0.2063	-0.0711	0.0607	0.1072	-0.0715	0.0012	0.4226	-0.0235	-0.043	0.2822	-0.0234	0.2971	68.743	91.813	34.301
18	0.0531	-0.0013	-0.0497	0.149	-0.058	-0.0181	0.1393	0.0607	0.4509	0.1505	0.214	-0.583	-0.3185	0.4724	0.0001	0.5779	-0.0231	0.1327	0.8973	-0.0713	0.7754	124.277	99.142	11.091
19	0.041	-0.0108	-0.1513	0.0001	0.1434	0.284	0.3251	0.5272	1.1017	0.2011	-0.2194	-0.5322	0.3817	0.9707	-0.0076	0.4326	-0.2373	-0.0912	0.739	0.2638	0.748	102.592	101.745	1.397
20	-0.0151	0.009	0.0043	-0.0022	-0.0162	0.0292	0.2718	0.2314	-0.2327	0.3744	-0.2814	0.0643	0.179	-0.6585	-0.0006	0.4259	-0.1501	0.0526	0.7836	-0.0332	0.6107	111.314	92.571	-2.892
21	0.0316	-0.0413	0.0407	0.0359	-0.0413	0.0341	0.1007	0.1172	0.0961	0.031	0.1012	0.2594	0.0192	0.1322	0.0002	0.7143	-0.3498	-0.1268	1.0095	0.2361	0.5812	98.83	94.927	-2.035
22	0.2373	-0.1842	-0.1616	0.2337	0.3295	0.5718	-0.2971	0.0919	0.4445	0.7574	0.4397	0.0103	-0.1192	0.5213	0.0229	0.464	-0.1159	0.0245	0.4446	0.1257	0.6395	105.309	96.016	9.6
23	0.6267	-0.6865	0.0517	1.2033	-0.1465	0.0188	0.2798	0.3909	-0.7495	-0.4951	-0.1582	0.6879	-0.0575	-0.3828	0.261	0.4051	-0.1346	0.2079	0.6254	0.08	0.6999	100.299	88.598	13.658
24	0.0387	0.0745	0.0261	0.0487	0.0631	0.0312	0.3402	0.2788	0.2045	0.158	0.3124	-0.4406	0.617	-0.0095	0.0031	0.4632	-0.0201	-0.0688	0.403	-0.0012	0.4477	104.742	83.287	14.373
25	0.0373	0.0335	-0.0241	0.5362	0.2968	0.1457	-0.2106	-0.7523	0.4243	-0.4415	-0.1024	-0.2466	-0.4689	0.2206	0.0083	0.5034	-0.0444	-0.0796	0.8447	-0.0428	0.5933	75.122	157.61	-9.422
26	0.0235	-0.0305	-0.0047	0.023	0.0005	0.0574	0.2172	0.2297	-0.127	0.0859	-0.5561	-0.0731	-0.0599	-0.3061	-0.0004	0.4997	0.0674	-0.0064	0.839	0.1073	0.7558	83.15	149.145	9.059
27	0.0058	-0.0013	-0.0104	0.0534	-0.0363	0.0061	-0.0584	0.0383	-0.0153	-0.0388	0.067	0.2272	-0.0819	-0.348	-0	0.5278	0.0414	0.0407	0.884	-0.1158	0.4557	91.447	147.568	9.447
28	0.0568	0.0655	-0.0596	0.0174	0.0076	0.0092	-0.2266	0.6129	-0.3582	0.0807	-0.2347	0.3226	-0.2124	0.2652	-0.0007	0.6668	0.1183	-0.059	0.8701	-0.0154	0.6224	84.577	140.779	3.203
29	0.0187	-0.034	0.0032	0.0188	-0.0021	-0.0033	0.0352	0.1459	-0.1857	-0.1663	0.2947	-0.6663	-0.3367	0.355	0.0002	0.539	0.185	0.1838	0.7801	0.0601	0.4858	91.716	150.767	-0.388
30	0.0788	-0.0594	0.0097	0.0214	-0.0079	-0	-0.3856	-0.632	0.1343	0.0442	0.3298	0.6325	0.0861	0.0759	-0.0001	0.4302	0.2018	-0.019	0.7504	-0.1901	0.5516	97.727	145.549	-4.716
31	0.5273	0.2501	0.3717	0.2316	0.3853	0.7658	-0.1438	0.2042	0.527	-0.2147	-0.8842	-0.4118	-0.1542	0.2352	-0.0472	0.635	0.2261	-0.0244	0.4609	0.1155	0.7903	99.726	145.085	-13.203

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 51:111 )	A	51 - 111
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 112:120 )	A	112 - 120
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 121:142 )	A	121 - 142
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 143:176 )	A	143 - 176
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 51:72 )	B	51 - 72
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 73:112 )	B	73 - 112
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 113:120 )	B	113 - 120
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 121:129 )	B	121 - 129
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 130:142 )	B	130 - 142
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 143:151 )	B	143 - 151
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 152:164 )	B	152 - 164
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 165:176 )	B	165 - 176
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 50:95 )	C	50 - 95
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 96:142 )	C	96 - 142
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 143:179 )	C	143 - 179
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 50:129 )	D	50 - 129
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 130:179 )	D	130 - 179
18	X-RAY DIFFRACTION	18	( CHAIN E AND RESID 52:71 )	E	52 - 71
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 72:96 )	E	72 - 96
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 97:120 )	E	97 - 120
21	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 121:129 )	E	121 - 129
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 130:142 )	E	130 - 142
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 143:161 )	E	143 - 161
24	X-RAY DIFFRACTION	24	( CHAIN E AND RESID 162:177 )	E	162 - 177
25	X-RAY DIFFRACTION	25	( CHAIN F AND RESID 51:72 )	F	51 - 72
26	X-RAY DIFFRACTION	26	( CHAIN F AND RESID 73:84 )	F	73 - 84
27	X-RAY DIFFRACTION	27	( CHAIN F AND RESID 85:96 )	F	85 - 96
28	X-RAY DIFFRACTION	28	( CHAIN F AND RESID 97:129 )	F	97 - 129
29	X-RAY DIFFRACTION	29	( CHAIN F AND RESID 130:142 )	F	130 - 142
30	X-RAY DIFFRACTION	30	( CHAIN F AND RESID 143:164 )	F	143 - 164
31	X-RAY DIFFRACTION	31	( CHAIN F AND RESID 165:178 )	F	165 - 178

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