PDB-4chb: Crystal structure of the human KLHL2 Kelch domain in complex with...

ID or keywords:

Entry

Database: PDB / ID: 4chb

Title

Crystal structure of the human KLHL2 Kelch domain in complex with a WNK4 peptide

Components

KELCH-LIKE PROTEIN 2
SERINE/THREONINE-PROTEIN KINASE WNK4

Keywords

SIGNALING PROTEIN/TRANSFERASE /

SIGNALING PROTEIN-TRANSFERASE COMPLEX / KLHL3 /

UBIQUITIN / ADAPTOR PROTEIN / PROTEIN-BINDING /

KELCH REPEAT / WNK SIGNALLING PATHWAY

Function / homology

Function and homology information

distal tubule morphogenesis / aldosterone secretion / renal sodium ion transport / regulation of potassium ion export across plasma membrane / negative regulation of pancreatic juice secretion / protein kinase C signaling / monoatomic ion homeostasis / negative regulation of sodium ion transport / intracellular chloride ion homeostasis / renal sodium ion absorption ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Sorrell, F.J. / Schumacher, F.R. / Kurz, T. / Alessi, D.R. / Newman, J. / Cooper, C.D.O. / Canning, P. / Kopec, J. / Williams, E. / Krojer, T. ...

Citation

Journal: Biochem.J. / Year: 2014
Title: Structural and Biochemical Characterisation of the Klhl3-Wnk Kinase Interaction Important in Blood Pressure Regulation.
Authors: Schumacher, F. / Sorrell, F.J. / Alessi, D.R. / Bullock, A.N. / Kurz, T.

History

Deposition	Nov 29, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2014	Group: Database references
Revision 1.2	May 28, 2014	Group: Database references
Revision 1.3	Jul 22, 2015	Group: Structure summary
Revision 1.4	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5	Mar 6, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6	May 29, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.7	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4chb.cif.gz	243.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4chb.ent.gz	196.4 KB	Display	PDB format
PDBx/mmJSON format	4chb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ch/4chb ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4chb	HTTPS FTP

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Related structure data

Related structure data	4ch9C 2xn4S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5nkp-2 7k2h-1 6qmc-d 6v6z-1 4ch9-2 5whl-1 6tki-d 7k2f-1 2iw3-d 2p1f-d 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	#60 - Dec 2004 Ubiquitin similarity (2) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1)

Deposited unit

A: KELCH-LIKE PROTEIN 2

B: KELCH-LIKE PROTEIN 2

C: SERINE/THREONINE-PROTEIN KINASE WNK4

D: SERINE/THREONINE-PROTEIN KINASE WNK4

hetero molecules

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

1

A: KELCH-LIKE PROTEIN 2

C: SERINE/THREONINE-PROTEIN KINASE WNK4

hetero molecules

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

2

B: KELCH-LIKE PROTEIN 2

D: SERINE/THREONINE-PROTEIN KINASE WNK4

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.700, 117.700, 106.650
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.1199, -0.9928, 0.002067), (-0.9928, 0.1199, -0.00021), (-4.0E-5, -0.002077, -1)
Vector: -58.48, -51.81, 1.651)

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein	KELCH-LIKE PROTEIN 2 / ACTIN-BINDING PROTEIN MAYVEN Mass: 32830.262 Da / Num. of mol.: 2 / Fragment: KELCH DOMAIN, RESIDUES 294-591 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: O95198
#2: Protein/peptide	SERINE/THREONINE-PROTEIN KINASE WNK4 / PROTEIN KINASE LYSINE-DEFICIENT 4 / PROTEIN KINASE WITH NO LYSINE 4 Mass: 1309.270 Da / Num. of mol.: 2 / Fragment: RESIDUES 557-567 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) References: UniProt: Q96J92, non-specific serine/threonine protein kinase

#1: Protein

KELCH-LIKE PROTEIN 2 / ACTIN-BINDING PROTEIN MAYVEN

Mass: 32830.262 Da / Num. of mol.: 2 / Fragment: KELCH DOMAIN, RESIDUES 294-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: O95198

#2: Protein/peptide

SERINE/THREONINE-PROTEIN KINASE WNK4 / PROTEIN KINASE LYSINE-DEFICIENT 4 / PROTEIN KINASE WITH NO LYSINE 4

Mass: 1309.270 Da / Num. of mol.: 2 / Fragment: RESIDUES 557-567 / Source method: obtained synthetically / Source: (synth.)

HOMO SAPIENS (human)
References: UniProt: Q96J92,

non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 307 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₅₀O₁₃ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.83 Å³/Da / Density % sol: 56.5 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: SITTING-DROP VAPOUR-DIFFUSION, 2.5 M AMMONIUM SULPHATE, 0.1 M HEPES, 2 % PEG 400 (PH 7.2), 293 K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.52→39.59 Å / Num. obs: 114962 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / R_merge(I) obs: 0.14 / Net I/σ(I): 7
Reflection shell	Resolution: 1.52→1.55 Å / Redundancy: 7 % / R_merge(I) obs: 1.1 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XN4

2xn4

Resolution: 1.56→39.516 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 17.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1935	5337	5 %
R_work	0.1771	-	-
obs	0.1779	106285	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.56→39.516 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4440	0	72	296	4808

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4804
X-RAY DIFFRACTION	f_angle_d	1.035	6554
X-RAY DIFFRACTION	f_dihedral_angle_d	11.06	1721
X-RAY DIFFRACTION	f_chiral_restr	0.044	716
X-RAY DIFFRACTION	f_plane_restr	0.005	862

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 (%)
1.56-1.5777	0.2627	167	0.2462	3330	X-RAY DIFFRACTION	100
1.5777-1.5963	0.2496	170	0.2329	3342	X-RAY DIFFRACTION	100
1.5963-1.6158	0.2119	172	0.2198	3323	X-RAY DIFFRACTION	100
1.6158-1.6362	0.2233	157	0.2126	3338	X-RAY DIFFRACTION	100
1.6362-1.6577	0.21	187	0.2111	3310	X-RAY DIFFRACTION	100
1.6577-1.6804	0.2263	170	0.2064	3334	X-RAY DIFFRACTION	100
1.6804-1.7045	0.2623	194	0.2056	3331	X-RAY DIFFRACTION	100
1.7045-1.7299	0.2217	172	0.1971	3321	X-RAY DIFFRACTION	100
1.7299-1.7569	0.218	174	0.1964	3327	X-RAY DIFFRACTION	100
1.7569-1.7857	0.2211	161	0.1831	3368	X-RAY DIFFRACTION	100
1.7857-1.8165	0.2222	163	0.1888	3326	X-RAY DIFFRACTION	100
1.8165-1.8496	0.2145	159	0.1837	3340	X-RAY DIFFRACTION	100
1.8496-1.8851	0.2036	182	0.1768	3317	X-RAY DIFFRACTION	100
1.8851-1.9236	0.1821	191	0.1609	3327	X-RAY DIFFRACTION	100
1.9236-1.9654	0.1705	151	0.1545	3379	X-RAY DIFFRACTION	100
1.9654-2.0112	0.1681	185	0.1561	3343	X-RAY DIFFRACTION	100
2.0112-2.0614	0.1695	195	0.1615	3344	X-RAY DIFFRACTION	100
2.0614-2.1172	0.1803	177	0.1605	3343	X-RAY DIFFRACTION	100
2.1172-2.1795	0.1966	189	0.1682	3338	X-RAY DIFFRACTION	100
2.1795-2.2498	0.1851	193	0.1716	3333	X-RAY DIFFRACTION	100
2.2498-2.3302	0.1914	185	0.1706	3380	X-RAY DIFFRACTION	100
2.3302-2.4235	0.188	174	0.1731	3353	X-RAY DIFFRACTION	100
2.4235-2.5338	0.1843	184	0.1768	3382	X-RAY DIFFRACTION	100
2.5338-2.6673	0.1966	205	0.1752	3364	X-RAY DIFFRACTION	100
2.6673-2.8344	0.1805	180	0.1782	3375	X-RAY DIFFRACTION	100
2.8344-3.0532	0.1896	189	0.1703	3401	X-RAY DIFFRACTION	100
3.0532-3.3603	0.1685	162	0.1757	3417	X-RAY DIFFRACTION	100
3.3603-3.8462	0.1881	186	0.1721	3434	X-RAY DIFFRACTION	100
3.8462-4.8444	0.1621	178	0.156	3484	X-RAY DIFFRACTION	100
4.8444-39.5284	0.232	185	0.1902	3644	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	3.7423	1.5955	-0.2335	3.9766	0.5237	2.2656	-0.119	-0.0474	0.024	-0.016	-0.0062	-0.1064	0.1395	0.143	0.13	0.0711	0.0158	-0.0017	0.1438	0.0173	0.069	-2.1648	-43.0647	-9.934
2	2.0356	-2.8923	0.1216	7.1095	3.4018	4.2736	-0.3372	-0.0754	-0.1146	-0.51	0.2847	-0.5353	0.2228	0.3669	0.0565	0.1988	0.0317	0.0682	0.2724	0.0409	0.1863	9.903	-42.5009	-13.1569
3	3.011	-0.0575	0.0644	0.1716	-0.0431	0.6526	-0.0335	-0.1636	0.0259	0.0219	0.0314	-0.0298	0.0025	0.0701	0.0115	0.0876	-0.0012	0.0012	0.1404	-0.0013	0.0517	-6.6835	-38.3895	-6.2413
4	4.3618	-0.7363	0.69	1.6656	0.1263	0.8045	-0.1316	-0.1563	0.1771	0.1566	0.0393	-0.1347	-0.283	0.1947	0.1205	0.1248	-0.0033	-0.0107	0.2187	-0.0125	0.0699	-5.6268	-32.0078	-1.0905
5	1.3904	0.0317	0.0797	1.4421	-0.0536	1.4239	-0.0163	-0.1686	0.1236	0.1139	0.0008	-0.0501	-0.1832	-0.0268	0.0211	0.0742	0.0179	-0.0014	0.0743	-0.0085	0.0652	-16.1764	-28.0323	-15.4506
6	1.286	-0.3469	-0.4489	1.4118	0.2759	1.1652	0.0382	0.0652	0.1273	-0.1063	-0.025	-0.1005	-0.121	-0.0217	-0.009	0.0786	0.0078	0.0127	0.0748	0.0158	0.0656	-12.0183	-31.0053	-29.3302
7	1.5258	0.4032	-0.2623	0.5541	0.1002	1.0088	-0.1553	-0.2799	-0.3266	-0.0643	-0.0411	-0.1813	0.2576	0.3375	0.1066	0.1064	0.0429	0.0351	0.1545	0.0405	0.1257	-0.4997	-43.9151	-25.4034
8	6.4862	3.32	0.9874	4.9742	1.6875	3.2875	0.1488	-0.2586	-0.0699	0.0406	-0.3079	-0.2893	0.0408	-0.0149	0.1408	0.0969	0.0487	-0.0013	0.2194	0.0554	0.1021	-2.9694	-40.7837	-13.8357
9	3.6216	1.1252	0.6315	2.9907	-0.1621	1.792	-0.0787	0.0092	-0.1236	-0.0604	-0.0482	-0.0799	0.2631	0.1385	0.1328	0.1934	0.0051	0.0189	0.0983	-0.0061	0.0619	-15.1817	-54.5698	11.7132
10	7.0872	-1.9014	-1.178	7.365	-1.6546	9.0035	0.1209	-0.4186	-0.3018	0.1213	0.0419	0.2854	0.1866	0.2099	-0.1561	0.1992	-0.0021	0.0141	0.1282	0.02	0.132	-15.8754	-66.0694	13.8105
11	1.2021	0.4866	-0.1153	2.5377	0.6275	1.3102	-0.0103	0.0978	-0.0363	-0.2094	-0.0045	0.054	0.1111	-0.0287	-0.0024	0.1482	-0.0085	-0.002	0.0952	0.0017	0.0476	-20.8337	-48.4167	7.1624
12	1.8047	-0.9153	0.0375	4.2924	2.2301	2.3292	0.1147	0.1152	-0.1369	-0.3594	-0.0913	0.1035	0.0204	-0.2341	0.0104	0.1835	-0.0183	-0.0159	0.1212	0.009	0.0728	-25.5455	-48.3631	2.3912
13	1.86	-0.1055	-0.0559	1.5305	-0.065	1.756	-0.0138	0.1383	-0.003	-0.1622	0.0184	0.0893	-0.0252	-0.0997	0.0066	0.0809	0.0102	-0.0085	0.0615	0.007	0.058	-28.7225	-39.2252	17.0527
14	4.5716	4.0951	-1.4816	3.6699	-1.3312	0.4826	-0.0231	-0.4218	0.618	0.4825	-0.3226	0.0855	-0.6684	0.3577	0.3507	0.2424	-0.0359	-0.0562	0.1493	-0.0014	0.1555	-18.1333	-32.362	29.6408
15	0.7837	-0.2457	0.0496	1.3545	-0.5784	1.0618	-0.0553	-0.1337	-0.0813	0.068	0.0375	0.0668	0.0003	-0.0169	0.0179	0.0761	0.007	0.0085	0.0663	0.0142	0.0577	-24.1014	-46.2956	30.5575
16	0.402	0.479	-0.3113	1.0722	-0.1051	1.5802	-0.1072	-0.0465	-0.2318	-0.4148	-0.1009	-0.2896	0.4194	0.3388	-0.0032	0.204	0.0414	0.0634	0.1301	0.0201	0.1256	-15.0248	-57.046	23.3921

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 306:323)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 324:331)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 332:373)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 374:388)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 389:459)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 460:524)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 525:578)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 579:591)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 306:323)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 324:335)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 336:376)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 377:388)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 389:458)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 459:463)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 464:542)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 543:591)

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-Experimental details

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

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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Non-polymers , 4 types, 307 molecules

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