PDB-5wg1: Kelch domain of human Keap1 bound to mutant Nrf2 EAGE peptide

ID or keywords:

Entry

Database: PDB / ID: 5wg1

Title

Kelch domain of human Keap1 bound to mutant Nrf2 EAGE peptide

Components

Kelch-like ECH-associated protein 1
Nrf2 EAGE mutant peptide

Keywords

TRANSCRIPTION /

Scaffold / Peptide-bound

Function / homology

Function and homology information

regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite /

inclusion body / cellular response to interleukin-4 /

regulation of autophagy /

actin filament / negative regulation of DNA-binding transcription factor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.021 Å

Authors

Carolan, J.P. / Lynch, A.J. / Allen, K.N.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2020
Title: Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).
Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / ...

History

Deposition	Jul 13, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 1, 2020	Group: Database references / Category: 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 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5wg1.cif.gz	239.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5wg1.ent.gz	192.9 KB	Display	PDB format
PDBx/mmJSON format	5wg1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/5wg1 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/5wg1	HTTPS FTP

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Related structure data

Related structure data	5wflSC 5wfvC 5whlC 5whoC 5wiyC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6zf2-d 7k2a-2 7k2g-1 5wfv-2 2z32-d 6sp1-1 7k2h-2 4zy3-2 6zex-d 6v6z-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#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

B: Kelch-like ECH-associated protein 1

P: Nrf2 EAGE mutant peptide

hetero molecules

75 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kelch-like ECH-associated protein 1

P: Nrf2 EAGE mutant peptide

hetero molecules

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

2

B: Kelch-like ECH-associated protein 1

hetero molecules

defined by author
37 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	161.809, 68.649, 77.126
Angle α, β, γ (deg.)	90.00, 117.54, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19 Mass: 36899.176 Da / Num. of mol.: 2 / Fragment: UNP residues 320-612 / Mutation: E540A, E542A Source method: isolated from a genetically manipulated source Details: His-tagged variant including mutations for altered crystallographic packing Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide	Nrf2 EAGE mutant peptide Mass: 1022.063 Da / Num. of mol.: 1 / Mutation: T80A / Source method: obtained synthetically / Details: Synthetic Nrf2 EAGE mutant peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.54 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1.2 - 1.5 M Ammonium sulfate, 0.1 M Bis-Tris pH = 6.0 - 6.5 PH range: 6.0 - 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Nitrogen stream
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2016 Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
Radiation	Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.021→34.32 Å / Num. obs: 46561 / % possible obs: 95 % / Redundancy: 2.5 % / CC_1/2: 0.971 / R_merge(I) obs: 0.1538 / Net I/σ(I): 6.27
Reflection shell	Resolution: 2.021→2.094 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.3269 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 4570 / CC_1/2: 0.862 / % possible all: 94

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WFL

5wfl

Resolution: 2.021→34.325 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2676	1994	4.28 %	Random selection
R_work	0.2319	-	-	-
obs	0.2334	46545	94.64 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.021→34.325 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4428	0	10	56	4494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4552
X-RAY DIFFRACTION	f_angle_d	0.688	6201
X-RAY DIFFRACTION	f_dihedral_angle_d	10.033	3568
X-RAY DIFFRACTION	f_chiral_restr	0.049	662
X-RAY DIFFRACTION	f_plane_restr	0.004	818

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 (%)
2.0214-2.0719	0.2485	137	0.2411	3096	X-RAY DIFFRACTION	94
2.0719-2.1279	0.2592	147	0.24	3147	X-RAY DIFFRACTION	95
2.1279-2.1905	0.2966	138	0.2482	3222	X-RAY DIFFRACTION	95
2.1905-2.2612	0.3123	138	0.2555	3100	X-RAY DIFFRACTION	93
2.2612-2.342	0.3034	134	0.2421	3080	X-RAY DIFFRACTION	91
2.342-2.4358	0.2586	140	0.2483	3238	X-RAY DIFFRACTION	97
2.4358-2.5466	0.3173	147	0.2691	3194	X-RAY DIFFRACTION	96
2.5466-2.6808	0.2943	142	0.2576	3231	X-RAY DIFFRACTION	96
2.6808-2.8487	0.2864	150	0.2533	3218	X-RAY DIFFRACTION	95
2.8487-3.0685	0.3288	135	0.2492	3108	X-RAY DIFFRACTION	92
3.0685-3.3771	0.2739	143	0.2432	3280	X-RAY DIFFRACTION	97
3.3771-3.8652	0.2601	149	0.231	3252	X-RAY DIFFRACTION	96
3.8652-4.8675	0.2166	148	0.1909	3162	X-RAY DIFFRACTION	93
4.8675-34.3294	0.2649	146	0.2266	3223	X-RAY DIFFRACTION	93

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	0.0319	0.0781	-0.0259	0.1172	-0.0333	0.0163	0.0019	0.8346	0.5937	-0.3337	0.0204	0.6558	-0.5951	-1.0407	0.051	0.4938	0.249	-0.1562	1.4989	0.724	0.7507	-54.9363	29.9374	48.5141
2	0.3101	-0.1123	0.1411	0.9086	-0.167	0.7769	-0.3868	2.4056	0.0667	0.1846	0.3088	0.4205	0.3574	-1.1336	-0.2307	0.044	-0.2443	-0.1655	1.8817	0.0475	0.5045	-53.8151	16.645	48.5466
3	1.0632	-0.2031	-0.489	1.5891	-0.4402	2.0506	-1.2252	1.4371	-1.1632	-0.1684	0.2536	0.1826	0.8912	-1.0413	-0.4956	0.3887	-0.3795	0.1367	0.9282	-0.2886	0.5817	-37.9098	11.6387	47.6871
4	1.8273	-0.0506	-0.4267	2.8372	0.1206	1.962	-0.5178	1.9226	-0.3742	-0.2614	0.2087	-0.103	0.3736	-0.6578	-0.0467	0.3245	-0.1763	0.0477	0.8829	-0.0381	0.5719	-29.4511	18.7499	42.1532
5	0.7377	-0.0765	-0.6049	0.0676	0.0002	0.5498	0.5227	1.1211	1.2392	-0.0985	0.4386	0.6289	-0.7982	-0.9854	0.7479	0.1925	0.1996	-0.0426	0.9732	0.5439	0.8242	-34.0626	31.4132	45.1255
6	0.2989	0.0211	-0.2951	0.5884	-1.2126	2.6602	0.2567	0.79	0.5014	-0.1287	-0.484	0.0274	-0.7101	-0.1106	-0.7157	0.6959	0.4449	0.2223	0.8573	1.3702	1.3063	-41.1629	37.9336	46.8914
7	0.4661	0.143	0.1419	0.6443	-0.4429	0.8053	0.0745	0.3647	0.2791	0.1513	0.1987	0.2301	-0.2106	-0.6263	0.0014	0.021	-0.2915	0.4276	1.4212	1.0849	0.4603	-50.506	29.5864	48.0249
8	2.5457	0.7028	0.458	2.8546	-0.6368	2.9048	0.0903	0.4583	0.0334	-0.1796	0.0201	0.1741	-0.0586	-0.09	-0.0297	0.2834	0.0004	-0.06	0.281	-0.0572	0.4232	-37.5506	16.8225	-2.7011
9	0.1822	0.2207	0.2859	0.6994	0.3192	1.7426	0.0405	0.178	-0.0099	-0.0482	-0.0552	0.1066	-0.0242	-0.2489	0.0337	0.2322	0.0072	-0.0443	0.3052	-0.0048	0.4069	-42.4115	17.9831	1.6573
10	2.6988	0.5386	1.3803	2.7623	0.5265	2.1282	-0.0515	0.3933	0.246	-0.3706	0.1607	0.0042	-0.1383	-0.2195	0.0442	0.3723	0.0358	-0.0517	0.3493	0.0032	0.4164	-39.895	27.4433	-1.8222
11	0.7596	-0.1726	0.2639	1.3605	-0.068	1.9958	-0.2884	-0.3731	0.1606	0.2501	0.1933	-0.2424	-0.1695	-0.1109	0.0467	0.2868	0.0689	-0.066	0.2911	-0.0094	0.3418	-33.9118	29.9084	10.3178
12	0.8282	-0.4907	0.6754	1.5218	-0.1471	2.2719	-0.2011	-0.4918	0.268	0.2949	0.1913	0.0594	-0.3244	-0.0649	0.0439	0.2934	0.0649	-0.0892	0.2858	-0.008	0.3655	-29.9091	30.5885	13.5856
13	0.3552	0.2286	0.5905	1.489	-0.0288	2.1777	-0.216	-0.1773	0.013	0.3132	0.1	-0.1325	-0.1435	-0.223	0.0121	0.2811	0.0504	-0.1025	0.2697	0.0006	0.3324	-23.2765	21.1578	17.4925
14	0.4145	0.4235	0.6601	1.5916	-0.5868	2.9637	-0.0227	-0.1478	-0.3485	0.1702	-0.151	-0.1577	-0.0224	0.2615	-0.053	0.2524	0.0272	-0.0669	0.2912	0.0513	0.3816	-20.3802	11.0517	15.0685
15	1.7037	-0.0163	0.1903	1.1866	-0.4446	2.7775	-0.19	-0.0432	-0.2786	0.0242	0.1948	-0.0792	0.3898	-0.2873	0.0149	0.2999	-0.0224	-0.0488	0.2758	0.0084	0.3874	-31.2929	7.7588	8.0544
16	0.1316	-0.117	0.3547	1.0606	-0.2411	2.333	0.0754	0.0345	-0.1884	-0.0155	-0.0143	0.0768	0.239	-0.1859	-0.0149	0.2654	-0.0363	-0.0429	0.2533	-0.0036	0.4129	-33.8717	8.0962	3.4671
17	0.5522	0.7072	-0.3448	1.6929	-1.4653	1.5492	0.2354	-0.343	0.0636	0.4049	-0.441	-0.0884	-0.1714	-0.3539	0.0139	0.5447	-0.0296	0.0959	0.6089	0.1009	0.7156	-42.1365	25.3738	63.5358

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 330 through 354 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 355 through 405 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 406 through 486 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 487 through 522 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 523 through 569 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 570 through 595 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 596 through 609 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 325 through 341 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 342 through 377 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 378 through 405 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 406 through 428 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 429 through 475 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 476 through 522 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 523 through 547 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 548 through 569 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 570 through 613 )
17	X-RAY DIFFRACTION	17	chain 'P' and (resid 76 through 84 )

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