PDB-4h3b: Crystal Structure of JNK3 in Complex with SAB Peptide

ID or keywords:

Entry

Database: PDB / ID: 4h3b

Title

Crystal Structure of JNK3 in Complex with SAB Peptide

Components

Mitogen-activated protein kinase 10
SH3 domain-binding protein 5

Keywords

TRANSFERASE / SH3BP-5 / MAPK /

kinase

Function / homology

Function and homology information

JUN kinase activity /

protein kinase inhibitor activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway /

MAP kinase kinase activity / response to light stimulus /

mitogen-activated protein kinase / JNK cascade / guanyl-nucleotide exchange factor activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.08 Å

Authors

Nwachukwu, J.C. / Laughlin, J.D. / Figuera-Losada, M. / Cherry, L. / Nettles, K.W. / LoGrasso, P.V.

Citation

Journal: Structure / Year: 2012
Title: Structural Mechanisms of Allostery and Autoinhibition in JNK Family Kinases.
Authors: Laughlin, J.D. / Nwachukwu, J.C. / Figuera-Losada, M. / Cherry, L. / Nettles, K.W. / Lograsso, P.V.

History

Deposition	Sep 13, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2012	Group: Database references
Revision 1.2	Dec 26, 2012	Group: Database references
Revision 1.3	Jun 17, 2015	Group: Structure summary
Revision 1.4	Sep 20, 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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Download

PDBx/mmCIF format	4h3b.cif.gz	312.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4h3b.ent.gz	254.8 KB	Display	PDB format
PDBx/mmJSON format	4h3b.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/h3/4h3b ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h3b	HTTPS FTP

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Related structure data

Related structure data	4h36C 4h39C 1jnkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3pze-d 4x21-1 2zdt-d 4z9l-d 3fi3-d 6emh-2 4ux9-2 3da6-d 2exc-d 1pmn-d 5r9o-d 3elj-d 3p78-d 4qtd-d 6emh-1 7ksk-d 3g9l-d 3v6r-1 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

Related structure data

4h36C

4h39C

1jnkS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Mitogen-activated protein kinase 10

B: SH3 domain-binding protein 5

C: Mitogen-activated protein kinase 10

D: SH3 domain-binding protein 5

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

1

A: Mitogen-activated protein kinase 10

B: SH3 domain-binding protein 5

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

2

C: Mitogen-activated protein kinase 10

D: SH3 domain-binding protein 5

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

Unit cell

Length a, b, c (Å)	84.520, 84.520, 127.250
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Mitogen-activated protein kinase 10 / MAP kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / ...MAP kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 Mass: 41180.641 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 45-400) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli) References: UniProt: P53779, mitogen-activated protein kinase
#2: Protein/peptide	SH3 domain-binding protein 5 / SH3BP-5 / SH3 domain-binding protein that preferentially associates with BTK Mass: 1053.233 Da / Num. of mol.: 2 / Fragment: UNP residues 341-350 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60239
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.11 Å³/Da / Density % sol: 60.45 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion / pH: 5.5 Details: 0.2 M sodium chloride, 0.1 M Bis-Tris, 28-31% PEG3350, pH 5.5, VAPOR DIFFUSION, temperature 294.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 1.17 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2011

Radiation

Monochromator: Side scattering bent-cube I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.17 Å / Relative weight: 1

Reflection

Resolution: 1.721→73.196 Å / Num. all: 107830 / Num. obs: 73519 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Net I/σ(I): 33.2

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
1.721-1.8	1	55.2
1.8-1.85	1	59.6
1.85-1.91	1	62.6
1.91-1.97	1	69.4
1.97-2.04	1	76.2
2.04-2.12	1	82.1
2.12-2.22	1	87.3
2.22-2.34	1	90.7
2.34-2.48	1	92.4
2.48-2.67	1	94.2
2.67-2.94	1	96.5
2.94-3.37	1	98.2
3.37-4.24	1	99.5
4.24-36.71	1	99.1

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHENIX	(phenix.refine: 1.7.1_743)	model building
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.7.1_743	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JNK

1jnk

Resolution: 2.08→36.7 Å / SU ML: 0.27 / σ(F): 0.11 / Phase error: 23.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	1027	1.79 %	RANDOM
R_work	0.1861	-	-	-
obs	0.187	57512	94.13 %	-
all	-	57512	-	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.602 Å² / k_sol: 0.33 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1039 Å²	0 Å²	0 Å²
2-	-	0.1039 Å²	-0 Å²
3-	-	-	-0.2078 Å²

Refinement step

Cycle: LAST / Resolution: 2.08→36.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5788	0	0	445	6233

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6036
X-RAY DIFFRACTION	f_angle_d	1.123	8199
X-RAY DIFFRACTION	f_dihedral_angle_d	13.779	2306
X-RAY DIFFRACTION	f_chiral_restr	0.083	912
X-RAY DIFFRACTION	f_plane_restr	0.005	1054

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 (%)
2.08-2.1897	0.322	126	0.2653	7357	X-RAY DIFFRACTION	86
2.1897-2.3269	0.2581	134	0.2167	7747	X-RAY DIFFRACTION	90
2.3269-2.5065	0.3036	145	0.2151	7899	X-RAY DIFFRACTION	92
2.5065-2.7587	0.2714	144	0.2149	8128	X-RAY DIFFRACTION	95
2.7587-3.1576	0.2341	166	0.1911	8336	X-RAY DIFFRACTION	98
3.1576-3.9775	0.2044	155	0.1703	8509	X-RAY DIFFRACTION	99
3.9775-36.7055	0.2139	157	0.1623	8509	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	2.8828	1.3918	1.3351	1.4379	1.2269	3.0501	-0.1933	-0.2411	-0.4078	0.2925	-0.0345	0.0401	0.5057	0.2221	0.0922	0.3197	0.0339	-0.0357	0.3715	0.1079	0.2851	-0.6765	-6.6281	10.0817
2	2.3936	0.1675	1.3381	1.6589	0.5878	3.385	-0.0978	0.2584	0.0203	-0.0987	-0.0852	0.1658	-0.0874	-0.0493	0.119	0.2184	-0.0129	-0.0141	0.441	0.0836	0.2092	-5.5391	1.2413	9.6215
3	0.8008	-0.3379	-1.1951	0.483	-0.5907	5.6539	-0.2081	0.0814	-0.2161	-0.2809	-0.0107	0.06	0.2068	-0.392	0.0726	0.2568	-0.076	0.0001	0.4105	0.0278	0.2072	-2.9248	1.5459	-3.4658
4	2.149	-0.0448	-1.7983	6.11	1.1431	4.6134	-0.1103	-0.0284	0.1333	-0.1269	0.0866	0.2785	-0.0727	-0.242	0.0322	0.2328	0.0793	0.0015	0.3958	-0.0067	0.2383	0.8989	10.3317	-4.7921
5	0.7066	-0.4047	0.0001	2.0995	0.0061	0.5589	0.0486	-0.0086	0.0644	-0.1954	-0.0874	-0.1625	0.0828	0.2064	0.0187	0.2165	0.084	-0.0042	0.4439	0.0015	0.2527	3.5334	9.4162	4.1334
6	3.5657	-0.7406	-2.1649	2.3548	1.1285	4.3864	0.0148	0.0831	-0.0474	-0.2823	-0.0062	-0.0843	0.1806	0.1079	-0.0197	0.2033	0.0252	-0.0175	0.3522	0.0611	0.2144	2.6119	-0.6413	0.4635
7	1.1433	-0.0882	0.0125	1.2043	-0.3052	0.4474	-0.2027	-0.4763	-0.072	0.2524	0.1554	0.0301	-0.2109	-0.3418	0.0506	0.2147	0.0568	0.0203	0.473	-0.0123	0.2462	-12.0728	21.6446	8.4421
8	1.4626	1.9122	0.3292	2.6243	0.4481	0.0751	-0.1388	0.3002	-0.4343	-0.2514	0.0141	0.3118	0.4338	-0.3294	0.0445	0.4047	-0.0485	0.0027	0.5067	-0.0126	0.4917	-10.264	10.6507	0.1477
9	1.1352	0.3095	-0.6171	0.8978	0.0364	1.6429	-0.1228	-0.1772	-0.0269	0.029	0.1895	0.0393	-0.011	-0.4671	-0.0248	0.1496	0.0757	0.0047	0.4479	0.0228	0.3041	-17.451	23.749	-4.0342
10	0.3305	-0.1281	0.0885	0.187	-0.0642	0.909	0.1244	-0.0491	-0.1627	-0.055	0.0253	0.1518	0.0406	-0.2545	0.233	0.1232	0.1381	0.019	0.8536	0.0106	0.2891	-28.0002	23.2809	-5.673
11	0.1451	-0.062	-0.0753	0.0708	0.0179	0.0503	-0.2133	-0.1461	0.187	0.1757	0.1442	0.0535	-0.2687	-0.4015	-0.295	0.1237	0.5673	0.1235	1.0336	0.0016	0.3086	-26.7778	33.8538	-9.7219
12	0.9841	0.1417	0.3716	0.7165	0.2004	0.663	0.0011	-0.2168	0.4479	0.2423	0.108	0.2479	-0.6409	-0.288	-0.1474	0.4643	0.2427	0.0389	0.4425	-0.0929	0.3787	-15.191	36.2024	5.4512
13	5.5548	-0.5504	-0.1399	5.8554	1.656	5.2966	0.1368	0.1628	0.2587	-0.211	0.013	-0.1831	-0.3469	0.0891	-0.112	0.4331	-0.0414	-0.0801	0.4723	-0.077	0.414	0.849	31.5405	10.5409
14	2.4698	0.0566	0.0687	3.6612	2.4499	6.226	0.158	-0.104	0.1394	-0.436	-0.004	-0.0286	0.1861	0.1439	-0.0735	0.4182	-0.0227	0.0431	0.6889	-0.0192	0.4007	4.6627	19.3761	-7.6136
15	3.3075	0.0299	0.9172	2.6583	-0.1331	6.0877	-0.313	-0.022	0.1104	-0.1147	0.0562	-0.254	-0.0605	0.3318	0.1277	0.3022	-0.0083	0.0982	0.4449	-0.0291	0.2503	8.2947	3.4761	-10.3739
16	0.7295	0.6234	0.0554	3.0749	-1.6165	3.2043	-0.0805	0.3052	-0.1459	-0.1577	-0.0821	0.3333	0.1157	-0.5975	0.0918	0.3434	0.0385	-0.0982	0.3584	-0.0359	0.2788	-5.4517	44.8967	-10.5414
17	1.6479	-0.2988	0.175	2.3334	-1.2471	2.9949	-0.181	-0.1565	-0.0958	0.2179	-0.0291	-0.0484	-0.0153	0.0228	0.1194	0.375	0.0995	-0.0949	0.2762	-0.0363	0.2182	3.8538	44.6481	-10.1584
18	0.5853	-0.2801	0.1931	0.3997	0.9558	4.6973	0.036	-0.1052	-0.1484	0.2574	-0.1787	0.1397	0.43	-0.0081	0.0321	0.4547	0.0308	-0.0162	0.2091	-0.0198	0.1912	2.5329	46.6568	2.3391
19	2.7323	0.1699	-2.4282	0.3801	0.3624	2.8347	0.089	-0.0619	-0.0864	0.0469	-0.1352	-0.025	0.0158	-0.0084	0.0404	0.3093	0.1098	-0.0122	0.3227	0.0093	0.2492	11.4254	56.5073	-0.0062
20	1.2212	-0.2111	-0.0651	2.0975	0.1916	2.2323	0.1647	-0.2097	0.2438	0.1344	-0.0184	0.1599	-0.1556	-0.4347	-0.0517	0.2868	0.0826	-0.0285	0.3192	-0.0208	0.2239	-2.6516	51.8508	-1.8038
21	0.8918	0.0725	0.3179	1.2479	-0.024	0.2375	0.158	0.4418	-0.0585	-0.2113	-0.1659	0.0436	0.2369	0.413	0.0371	0.3448	0.1456	0.0179	0.3348	-0.0167	0.2417	24.8806	48.7125	-9.2561
22	0.9486	1.636	-0.2698	2.8253	-0.4666	0.1012	-0.0068	-0.1591	-0.4205	0.2856	-0.0731	0.184	0.4236	-0.2534	0.0239	0.4952	0.0305	0.0034	0.3884	-0.0037	0.4896	14.3548	45.2216	-0.6609
23	0.8558	-0.157	-0.3269	1.3274	0.0964	1.797	0.1697	0.204	-0.0055	-0.037	-0.1355	-0.0555	0.4545	0.237	-0.0205	0.3168	0.1577	-0.0097	0.2851	-0.0214	0.3029	29.125	45.6714	3.8233
24	1.2861	-0.6625	-1.2004	0.4511	1.0541	2.8808	-0.0593	-0.2105	-0.0955	0.1654	0.1703	-0.1223	0.3457	0.142	0.1773	0.6582	0.3924	-0.0175	0.4646	-0.0915	0.3164	33.2863	35.6317	-0.495
25	0.7066	-0.3677	-0.3184	0.4118	0.1783	0.1541	0.1095	0.0544	0.1017	0.0684	0.0047	-0.2088	0.1035	0.2959	-0.0568	0.4437	0.3992	0.0155	0.5399	-0.047	0.3472	39.2192	42.9382	12.8219
26	0.0014	-0.0171	-0.0027	-0.004	0.0028	-0.0002	0.0744	0.243	0.0027	-0.0289	-0.0951	-0.1321	0.1671	0.2363	-0.0685	0.4935	0.807	0.0361	0.839	-0.057	0.3362	43.4782	40.1181	10.3514
27	0.9779	-0.3773	-0.5244	1.3185	0.1177	0.3102	0.0949	0.2498	0.0208	-0.2475	-0.0379	-0.435	0.0171	0.7246	-0.1993	0.2466	0.1412	0.0913	0.6778	0.0284	0.3681	40.093	50.7009	-5.5628
28	2.985	-1.7145	0.1822	1.3498	-0.2965	0.1172	-0.1174	0.031	0.3488	-0.0715	0.1932	-0.1334	-0.2993	0.4178	-0.056	0.4468	0.0403	0.1001	0.6053	0.1015	0.3777	32.0684	61.0617	-11.9322
29	3.4483	0.7415	-1.7364	2.265	-0.6076	5.077	0.2227	-0.4018	0.0771	-0.0092	-0.0903	-0.0711	0.0044	-0.2341	-0.0533	0.6021	0.0881	0.0337	0.4332	-0.0239	0.4024	14.4181	62.5334	7.0721
30	2.7178	-0.407	0.6033	3.4211	-1.322	6.7918	0.0065	0.1646	0.2522	0.0639	-0.3243	0.0269	-0.3827	-0.1247	0.1823	0.4261	0.0497	0.0562	0.3421	-0.0707	0.2562	-1.1379	57.7128	9.8362

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 45:68)
2	X-RAY DIFFRACTION	2	(chain A and resid 69:87)
3	X-RAY DIFFRACTION	3	(chain A and resid 88:106)
4	X-RAY DIFFRACTION	4	(chain A and resid 107:115)
5	X-RAY DIFFRACTION	5	(chain A and resid 116:135)
6	X-RAY DIFFRACTION	6	(chain A and resid 136:148)
7	X-RAY DIFFRACTION	7	(chain A and resid 149:203)
8	X-RAY DIFFRACTION	8	(chain A and resid 204:221)
9	X-RAY DIFFRACTION	9	(chain A and resid 222:257)
10	X-RAY DIFFRACTION	10	(chain A and resid 258:276)
11	X-RAY DIFFRACTION	11	(chain A and resid 277:319)
12	X-RAY DIFFRACTION	12	(chain A and resid 325:362)
13	X-RAY DIFFRACTION	13	(chain A and resid 363:370)
14	X-RAY DIFFRACTION	14	(chain A and resid 371:382)
15	X-RAY DIFFRACTION	15	(chain A and resid 383:400)
16	X-RAY DIFFRACTION	16	(chain C and resid 45:68)
17	X-RAY DIFFRACTION	17	(chain C and resid 69:87)
18	X-RAY DIFFRACTION	18	(chain C and resid 88:105)
19	X-RAY DIFFRACTION	19	(chain C and resid 106:125)
20	X-RAY DIFFRACTION	20	(chain C and resid 126:148)
21	X-RAY DIFFRACTION	21	(chain C and resid 149:203)
22	X-RAY DIFFRACTION	22	(chain C and resid 204:221)
23	X-RAY DIFFRACTION	23	(chain C and resid 222:256)
24	X-RAY DIFFRACTION	24	(chain C and resid 257:267)
25	X-RAY DIFFRACTION	25	(chain C and resid 268:292)
26	X-RAY DIFFRACTION	26	(chain C and resid 293:314)
27	X-RAY DIFFRACTION	27	(chain C and resid 315:354)
28	X-RAY DIFFRACTION	28	(chain C and resid 355:370)
29	X-RAY DIFFRACTION	29	(chain C and resid 371:382)
30	X-RAY DIFFRACTION	30	(chain C and resid 383:400)

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