PDB-4h39: Crystal Structure of JNK3 in Complex with JIP1 Peptide

ID or keywords:

Entry

Database: PDB / ID: 4h39

Title

Crystal Structure of JNK3 in Complex with JIP1 Peptide

Components

C-Jun-amino-terminal kinase-interacting protein 1
Mitogen-activated protein kinase 10

Keywords

TRANSFERASE / MAPK /

kinase

Function / homology

Function and homology information

dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / JUN kinase activity / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding /

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

MAP kinase kinase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.992 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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PDBx/mmCIF format	4h39.cif.gz	158.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4h39.ent.gz	124.7 KB	Display	PDB format
PDBx/mmJSON format	4h39.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/h3/4h39 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h39	HTTPS FTP

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Related structure data

Related structure data	4h36C 4h3bC 1jnkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3v6s-2 3ldf-d 4hys-d 2ghb-1 4hyu-d 3v6r-2 3vse-1 3vse-3 3heg-d 4h36-d 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	#88 - Apr 2007 Clathrin similarity (4) #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: C-Jun-amino-terminal kinase-interacting protein 1

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	63.206, 83.711, 83.917
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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.: 1 / Fragment: catalytic domain (UNP residues 45-400) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JNK3, JNK3A, MAPK10, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli) References: UniProt: P53779, mitogen-activated protein kinase
#2: Protein/peptide	C-Jun-amino-terminal kinase-interacting protein 1 / JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / ...JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1 Mass: 1188.418 Da / Num. of mol.: 1 / Fragment: UNP residues 158-167 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQF2
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.62 Å³/Da / Density % sol: 53.1 %
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 294K

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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: 1.992→37.51 Å / Num. all: 29692 / Num. obs: 29642 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Net I/σ(I): 49.3

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
1.992-2.09	1	81.9
2.09-2.15	1	85.3
2.15-2.21	1	84.9
2.21-2.28	1	44.2
2.28-2.36	1	86
2.36-2.46	1	93.4
2.46-2.57	1	95.7
2.57-2.7	1	96.5
2.7-2.87	1	97.3
2.87-3.09	1	98.6
3.09-3.41	1	99.2
3.41-3.9	1	81.9
3.9-4.91	1	99.4
4.91-37.52	1	98.9

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHENIX	(phenix.automr: 1.7.1_743)	model building
PHENIX	(phenix.refine: 1.7.1_743)	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: 1.992→37.51 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 25.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2387	1931	6.76 %	RANDOM
R_work	0.2092	-	-	-
all	0.2113	29642	-	-
obs	0.2113	28561	91.84 %	-

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.555 Å² / k_sol: 0.319 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.5662 Å²	0 Å²	-0 Å²
2-	-	2.3646 Å²	-0 Å²
3-	-	-	-6.9308 Å²

Refinement step

Cycle: LAST / Resolution: 1.992→37.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2773	0	0	154	2927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2842
X-RAY DIFFRACTION	f_angle_d	0.72	3867
X-RAY DIFFRACTION	f_dihedral_angle_d	12.975	1055
X-RAY DIFFRACTION	f_chiral_restr	0.053	438
X-RAY DIFFRACTION	f_plane_restr	0.003	497

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 (%)
1.992-2.042	0.3348	128	0.255	1711	X-RAY DIFFRACTION	84
2.042-2.0972	0.2802	137	0.2375	1897	X-RAY DIFFRACTION	93
2.0972-2.159	0.2695	137	0.2287	1894	X-RAY DIFFRACTION	94
2.159-2.2286	0.2956	131	0.25	1726	X-RAY DIFFRACTION	86
2.2286-2.3083	0.4995	79	0.3687	1114	X-RAY DIFFRACTION	55
2.3083-2.4007	0.2765	145	0.2381	1988	X-RAY DIFFRACTION	97
2.4007-2.5099	0.2448	148	0.2309	2003	X-RAY DIFFRACTION	98
2.5099-2.6422	0.3055	147	0.2341	2057	X-RAY DIFFRACTION	99
2.6422-2.8077	0.2956	142	0.2201	2027	X-RAY DIFFRACTION	99
2.8077-3.0244	0.2623	150	0.2259	2061	X-RAY DIFFRACTION	99
3.0244-3.3286	0.2432	151	0.2098	2076	X-RAY DIFFRACTION	100
3.3286-3.8098	0.1988	122	0.2002	1757	X-RAY DIFFRACTION	84
3.8098-4.7984	0.1753	152	0.1702	2122	X-RAY DIFFRACTION	100
4.7984-37.517	0.2274	162	0.1957	2197	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	1.4126	-0.8781	-0.851	5.6791	0.6216	6.7272	-0.3224	-0.3744	-0.1356	0.2883	0.532	-0.6868	-0.0287	0.7878	0.0489	0.3452	0.1069	-0.0437	0.4127	-0.0138	0.338	13.5733	-11.0903	-8.2474
2	4.8824	-0.3036	-2.1116	5.0724	-0.3003	3.8389	-0.1267	-0.1897	0.1924	0.1129	0.0748	0.2055	0.1228	-0.0826	-0.048	0.2917	-0.0073	-0.0269	0.2266	0.0096	0.2806	6.1087	-4.7178	-6.9274
3	2.4005	-0.5484	-1.7741	2.9442	-1.5873	4.2134	0.0072	0.2555	0.1927	-0.4987	-0.0263	-0.07	0.091	-0.1869	-0.1444	0.3449	-0.0271	-0.0033	0.3683	0.0106	0.4169	9.1177	-0.7707	-22.4003
4	1.9226	-0.3148	0.7888	1.6028	-0.9603	0.7451	0.0952	0.1781	0.0829	-0.0854	0.0197	-0.4655	-0.3589	0.4181	0.0969	0.3511	0.0162	-0.0528	0.3749	-0.0189	0.4195	2.2583	11.9319	-15.0571
5	4.3975	-1.044	0.05	4.1125	-0.0783	3.8043	0.4025	0.2652	0.0638	-0.5555	-0.1113	-0.4972	0.1178	0.3994	0.055	0.3599	-0.0191	-0.0144	0.3524	0.0266	0.4101	16.8642	-2.0479	-15.6946
6	5.898	-3.5834	3.3121	3.0278	-0.8784	3.9734	-0.0157	-0.4381	-0.1214	-0.0876	0.0753	0.1431	0.2791	-0.5488	-0.1915	0.46	0.0094	0.0342	0.3424	0.0755	0.3949	-11.2589	2.1383	-11.5746
7	4.8515	-2.0913	1.0778	2.4949	2.0497	4.6924	-0.9152	-0.3096	-0.662	0.2189	0.4811	0.9102	-0.1273	-0.5309	-0.1347	0.6674	-0.0028	0.1144	0.547	0.137	0.4689	-23.9015	9.1571	-9.6107
8	2.0258	-0.6885	0.6506	2.9361	-1.253	1.9878	0.0011	-0.2006	-0.0551	0.2235	-0.0005	-0.1552	-0.1995	0.0529	0.1056	0.3287	0.022	-0.0179	0.2606	-0.0042	0.3067	-9.2263	11.8248	-16.6755
9	0.2808	-1.0882	0.1411	4.3382	-1.1013	5.0388	-0.3271	1.2826	-0.2323	0.2846	1.1871	0.2304	2.3036	-1.7253	-0.1861	1.115	-0.2915	0.149	0.9805	0.0741	0.6698	-8.8557	0.9122	-23.2501
10	3.4763	0.8868	0.611	2.4241	-0.4901	5.9203	0.0451	0.2081	-0.3643	-0.1015	0.1679	-0.2853	0.5095	-0.1515	-0.1902	0.3062	0.0233	-0.0249	0.2387	-0.0328	0.3258	-16.9391	8.6324	-28.6071
11	4.2179	0.9011	0.0129	3.2028	1.9418	7.5888	0.1784	0.6302	-0.0496	-0.2719	0.1537	-0.0964	-0.0689	-0.258	-0.068	0.2879	-0.0212	0.0088	0.3855	-0.0891	0.2948	-22.683	9.3197	-42.3972
12	4.0546	1.2611	0.7185	3.6366	0.3208	4.8301	0.3013	-0.5292	0.1942	0.7682	-0.2261	0.8062	-0.5006	-1.486	0.2273	0.4511	-0.0299	0.0548	0.7163	0.0225	0.452	-31.9228	14.8978	-19.2503
13	1.1324	-0.29	0.4139	2.0465	0.8195	5.0115	-0.1637	-0.1182	0.2464	0.1308	0.0485	-0.0182	-0.5411	-0.1139	0.0712	0.3751	0.0644	-0.0065	0.2585	-0.0291	0.3157	-17.8507	21.5587	-20.8047
14	5.4416	-4.5805	-0.1664	6.9499	-0.3536	2.8935	0.6127	0.0983	0.755	-0.8331	-0.5624	-0.4495	-0.3304	0.0309	0.232	0.6937	-0.163	0.0457	0.5551	0.0093	0.5101	9.029	13.2988	-27.804
15	5.6474	-1.9802	1.5768	5.4393	-1.1883	7.2565	-0.3422	0.3457	0.5237	-0.1171	-0.018	-0.7277	-0.3851	1.1669	0.2706	0.3712	-0.0474	0.0395	0.5332	0.0838	0.5183	19.4533	4.0894	-22.9853
16	8.863	-3.9059	0.0701	5.9671	1.4662	9.8294	-0.6248	-0.1153	-0.5372	1.7655	0.2821	1.1278	0.2787	-1.135	0.4251	0.4577	0.0618	0.1239	0.5834	0.0037	0.3273	-16.3677	10.7683	-3.4081

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 45:57)
2	X-RAY DIFFRACTION	2	(chain A and resid 58:87)
3	X-RAY DIFFRACTION	3	(chain A and resid 88:113)
4	X-RAY DIFFRACTION	4	(chain A and resid 114:127)
5	X-RAY DIFFRACTION	5	(chain A and resid 128:146)
6	X-RAY DIFFRACTION	6	(chain A and resid 147:157)
7	X-RAY DIFFRACTION	7	(chain A and resid 158:164)
8	X-RAY DIFFRACTION	8	(chain A and resid 165:205)
9	X-RAY DIFFRACTION	9	(chain A and resid 206:227)
10	X-RAY DIFFRACTION	10	(chain A and resid 228:267)
11	X-RAY DIFFRACTION	11	(chain A and resid 268:306)
12	X-RAY DIFFRACTION	12	(chain A and resid 307:328)
13	X-RAY DIFFRACTION	13	(chain A and resid 329:368)
14	X-RAY DIFFRACTION	14	(chain A and resid 369:387)
15	X-RAY DIFFRACTION	15	(chain A and resid 388:400)
16	X-RAY DIFFRACTION	16	(chain B and resid 158:167)

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