PDB-6tg8: Crystal structure of the Kelch domain in complex with 11 amino ac...

ID or keywords:

Entry

Database: PDB / ID: 6tg8

Title

Crystal structure of the Kelch domain in complex with 11 amino acid peptide (model of the ETGE loop)

Components

Kelch-like ECH-associated protein 1
VAL-ILE-ASN-PRO-GLU-THR-GLY-GLU-GLN-ILE-GLN

Keywords

LIGASE /

complex / beta proteins /

Kelch motif

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: 2.75 Å

Authors

Kekez, I. / Matic, S. / Tomic, S. / Matkovic-Calogovic, D.

Funding support

Croatia, 1items

Citation

Journal: J.Biomol.Struct.Dyn. / Year: 2021
Title: Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process.
Authors: Matic, S. / Kekez, I. / Tomin, M. / Bogar, F. / Supljika, F. / Kazazic, S. / Hanic, M. / Jha, S. / Brkic, H. / Bourgeois, B. / Madl, T. / Gruber, K. / Macheroux, P. / Matkovic-Calogovic, D. ...

History

Deposition	Nov 15, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 23, 2020	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 27, 2021	Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Jan 24, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tg8.cif.gz	75.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6tg8.ent.gz		Display	PDB format
PDBx/mmJSON format	6tg8.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/tg/6tg8 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/6tg8	HTTPS FTP

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Related structure data

Related structure data	1zgkS S: Starting model for refinement
Similar structure data	2iax-d 3hli-4 2iao-d 4in4-1 2gvx-d 2gvu-d 3hlh-3 3vng-d 1dwc-d 1ucy-2 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

AAA: Kelch-like ECH-associated protein 1

PPP: VAL-ILE-ASN-PRO-GLU-THR-GLY-GLU-GLN-ILE-GLN

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	75.296, 75.296, 127.539
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19 Mass: 31583.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide	VAL-ILE-ASN-PRO-GLU-THR-GLY-GLU-GLN-ILE-GLN Mass: 1227.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.18 Å³/Da / Density % sol: 61.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 M sodium acetate pH 7.0, 0.1 M Bis-Tris propane pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 4, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.45→65.208 Å / Num. obs: 11948 / % possible obs: 99.5 % / Redundancy: 18.1 % / R_merge(I) obs: 0.11 / Net I/σ(I): 40.66
Reflection shell	Resolution: 2.7→2.8 Å / R_merge(I) obs: 0.614 / Num. unique obs: 1198

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
CrysalisPro	1.171.40.53	data reduction
Aimless	7.0.077	data scaling
AMoRE	7.0.077	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1zgk

1zgk

Resolution: 2.75→17 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.923 / SU B: 18.237 / SU ML: 0.321 / Cross valid method: FREE R-VALUE / ESU R: 0.651 / ESU R Free: 0.337
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2584	560	4.951 %
R_work	0.181	-	-
all	0.185	-	-
obs	-	11310	99.49 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 69.133 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.06 Å²	-0.03 Å²	-0 Å²
2-	-	-0.06 Å²	0 Å²
3-	-	-	0.196 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2302	0	1	9	2312

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	2381
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	2111
X-RAY DIFFRACTION	r_angle_refined_deg	1.499	1.644	3246
X-RAY DIFFRACTION	r_angle_other_deg	1.212	1.572	4871
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.742	5	303
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.296	20.657	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.645	15	356
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.114	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	298
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2771
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	546
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	446
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	2181
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	1117
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1125
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.129	0.2	45
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.243	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	17
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.215	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.891	7.152	1206
X-RAY DIFFRACTION	r_mcbond_other	4.874	7.148	1205
X-RAY DIFFRACTION	r_mcangle_it	7.247	10.73	1508
X-RAY DIFFRACTION	r_mcangle_other	7.246	10.736	1509
X-RAY DIFFRACTION	r_scbond_it	5.518	7.848	1175
X-RAY DIFFRACTION	r_scbond_other	5.494	7.841	1173
X-RAY DIFFRACTION	r_scangle_it	8.655	11.528	1737
X-RAY DIFFRACTION	r_scangle_other	8.647	11.529	1737
X-RAY DIFFRACTION	r_lrange_it	10.99	82.487	2556
X-RAY DIFFRACTION	r_lrange_other	10.988	82.533	2557

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 (%)
2.75-2.82	0.39	33	0.39	769	X-RAY DIFFRACTION	100
2.82-2.896	0.388	28	0.341	781	X-RAY DIFFRACTION	100
2.896-2.978	0.468	34	0.315	703	X-RAY DIFFRACTION	100
2.978-3.067	0.283	34	0.288	717	X-RAY DIFFRACTION	100
3.067-3.165	0.431	48	0.262	676	X-RAY DIFFRACTION	100
3.165-3.274	0.31	43	0.25	677	X-RAY DIFFRACTION	100
3.274-3.394	0.332	27	0.23	629	X-RAY DIFFRACTION	100
3.394-3.528	0.33	35	0.215	637	X-RAY DIFFRACTION	100
3.528-3.68	0.287	42	0.198	581	X-RAY DIFFRACTION	100
3.68-3.853	0.288	29	0.178	578	X-RAY DIFFRACTION	100
3.853-4.053	0.176	26	0.164	565	X-RAY DIFFRACTION	100
4.053-4.288	0.163	19	0.12	528	X-RAY DIFFRACTION	100
4.288-4.569	0.186	33	0.114	482	X-RAY DIFFRACTION	100
4.569-4.914	0.169	36	0.105	460	X-RAY DIFFRACTION	100
4.914-5.35	0.231	16	0.118	449	X-RAY DIFFRACTION	100
5.35-5.929	0.282	18	0.159	405	X-RAY DIFFRACTION	100
5.929-6.748	0.296	20	0.189	355	X-RAY DIFFRACTION	100
6.748-8.039	0.255	19	0.201	308	X-RAY DIFFRACTION	100
8.039-10.549	0.213	14	0.148	267	X-RAY DIFFRACTION	100
10.549-17.813	0.306	4	0.2	181	X-RAY DIFFRACTION	92.9648

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