PDB-8rpp: Crystal structure of the JIP1-JIP2-SH3 heterodimer and the JIP2-J...

ID or keywords:

Entry

Database: PDB / ID: 8rpp

Title

Crystal structure of the JIP1-JIP2-SH3 heterodimer and the JIP2-JIP2-SH3 homodimer

Components

C-Jun-amino-terminal kinase-interacting protein 1
C-Jun-amino-terminal kinase-interacting protein 2

Keywords

SIGNALING PROTEIN / Regulation of JNK cascade

Function / homology

Function and homology information

nonassociative learning / dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of stress-activated MAPK cascade / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / regulation of AMPA receptor activity / JUN kinase binding / signal complex assembly / regulation of signaling receptor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.867 Å

Authors

Palencia, A. / Marino-Perez, L. / Ielasi, F.I. / Jensen, M.R.

Funding support

France, 5items

Organization	Grant number	Country
Agence Nationale de la Recherche (ANR)	ScaffoldDisorder	France
Agence Nationale de la Recherche (ANR)	Impulscience	France
Agence Nationale de la Recherche (ANR)	ANR-17-EURE-0003	France
Agence Nationale de la Recherche (ANR)	ANR-10-INBS-0005-02	France
Fondation pour la Recherche Medicale (FRM)	SPF201909009258	France

Citation

Journal: Structure / Year: 2024
Title: Structural basis of homodimerization of the JNK scaffold protein JIP2 and its heterodimerization with JIP1
Authors: Palencia, A. / Marino-Perez, L. / Ielasi, F.I. / Jensen, M.R. / Lee, A. / Delaforge, E. / Juyoux, P. / Davis, R.G.

History

Deposition	Jan 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8rpp.cif.gz	70.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8rpp.ent.gz	50.6 KB	Display	PDB format
PDBx/mmJSON format	8rpp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8rpp_validation.pdf.gz	433.8 KB	Display	wwPDB validaton report
Full document	8rpp_full_validation.pdf.gz	434.6 KB	Display
Data in XML	8rpp_validation.xml.gz	12.5 KB	Display
Data in CIF	8rpp_validation.cif.gz	17.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rp/8rpp ftp://data.pdbj.org/pub/pdb/validation_reports/rp/8rpp	HTTPS FTP

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Related structure data

Related structure data	7nyk
Similar structure data	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)

Deposited unit

A: C-Jun-amino-terminal kinase-interacting protein 2

B: C-Jun-amino-terminal kinase-interacting protein 2

C: C-Jun-amino-terminal kinase-interacting protein 2

D: C-Jun-amino-terminal kinase-interacting protein 1

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

1

A: C-Jun-amino-terminal kinase-interacting protein 2

D: C-Jun-amino-terminal kinase-interacting protein 1

defined by author&software
Evidence: gel filtration, NMR relaxation study, assay for oligomerization
14.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: C-Jun-amino-terminal kinase-interacting protein 2

C: C-Jun-amino-terminal kinase-interacting protein 2

defined by author&software
Evidence: NMR relaxation study, gel filtration
14.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.470, 68.470, 177.259
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-745- HOH
2	1	B-756- HOH
3	1	B-757- HOH
4	1	D-637- HOH

#1: Protein	C-Jun-amino-terminal kinase-interacting protein 2 / JIP-2 / JNK-interacting protein 2 / Islet-brain-2 / IB-2 / JNK MAP kinase scaffold protein 2 / ...JIP-2 / JNK-interacting protein 2 / Islet-brain-2 / IB-2 / JNK MAP kinase scaffold protein 2 / Mitogen-activated protein kinase 8-interacting protein 2 Mass: 7413.202 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: GRR is part of the purification tag / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP2, IB2, JIP2, PRKM8IPL / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q13387
#2: Protein	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: 7296.083 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GHM is part of the purification tag / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP1, IB1, JIP1, PRKM8IP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UQF2
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.8 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Malonate 1.5 M

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2021
Radiation	Monochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96546 Å / Relative weight: 1
Reflection	Resolution: 1.867→59.086 Å / Num. obs: 25670 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.062 / R_rim(I) all: 0.098 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.867→1.899 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1340 / CC_1/2: 0.76 / R_pim(I) all: 0.332 / R_rim(I) all: 0.644 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
AutoProcess	1.1.7	data reduction
STARANISO	2.3.73	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.867→59.086 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.957 / SU B: 2.733 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1936	1283	4.999 %
R_work	0.1482	24380	-
all	0.15	-	-
obs	-	25663	99.577 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.922 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.255 Å²	0.128 Å²	-0 Å²
2-	-	0.255 Å²	0 Å²
3-	-	-	-0.828 Å²

Refinement step

Cycle: LAST / Resolution: 1.867→59.086 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2038	0	0	182	2220

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2141
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1819
X-RAY DIFFRACTION	r_angle_refined_deg	1.538	1.651	2915
X-RAY DIFFRACTION	r_angle_other_deg	0.525	1.553	4226
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.896	5	249
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.022	10	27
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.729	10	312
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.801	10	137
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	286
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2575
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	509
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	367
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	1847
X-RAY DIFFRACTION	r_nbtor_refined	0.192	0.2	1020
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	1130
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	149
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.345	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.164	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.127	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	2.096	2.382	984
X-RAY DIFFRACTION	r_mcbond_other	2.096	2.382	984
X-RAY DIFFRACTION	r_mcangle_it	3.071	3.549	1228
X-RAY DIFFRACTION	r_mcangle_other	3.07	3.552	1229
X-RAY DIFFRACTION	r_scbond_it	3.478	2.763	1157
X-RAY DIFFRACTION	r_scbond_other	3.476	2.764	1158
X-RAY DIFFRACTION	r_scangle_it	5.392	4.006	1684
X-RAY DIFFRACTION	r_scangle_other	5.39	4.007	1685
X-RAY DIFFRACTION	r_lrange_it	6.931	37.128	2395
X-RAY DIFFRACTION	r_lrange_other	6.905	36.144	2370

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.867-1.916	0.304	93	0.211	1830	0.215	1928	0.944	0.969	99.7407	0.2
1.916-1.968	0.206	76	0.195	1784	0.196	1865	0.973	0.976	99.7319	0.184
1.968-2.025	0.246	78	0.185	1705	0.188	1784	0.967	0.978	99.9439	0.172
2.025-2.087	0.255	57	0.169	1699	0.172	1765	0.962	0.982	99.4901	0.158
2.087-2.156	0.213	100	0.165	1608	0.168	1715	0.97	0.983	99.5918	0.15
2.156-2.231	0.177	126	0.154	1484	0.156	1617	0.98	0.983	99.5671	0.141
2.231-2.315	0.212	94	0.149	1484	0.153	1583	0.974	0.986	99.6841	0.137
2.315-2.41	0.213	69	0.165	1456	0.167	1531	0.974	0.984	99.6081	0.151
2.41-2.517	0.229	88	0.159	1357	0.163	1455	0.971	0.985	99.3127	0.146
2.517-2.639	0.236	49	0.154	1360	0.157	1415	0.963	0.985	99.576	0.145
2.639-2.782	0.226	63	0.149	1236	0.153	1303	0.972	0.986	99.693	0.143
2.782-2.95	0.195	81	0.15	1189	0.153	1274	0.978	0.986	99.686	0.147
2.95-3.153	0.204	65	0.148	1108	0.151	1177	0.975	0.987	99.6601	0.148
3.153-3.405	0.207	49	0.139	1064	0.141	1114	0.978	0.989	99.9102	0.142
3.405-3.729	0.147	42	0.127	963	0.128	1008	0.991	0.991	99.7024	0.138
3.729-4.167	0.136	28	0.112	875	0.113	913	0.992	0.993	98.9047	0.129
4.167-4.807	0.141	53	0.101	747	0.103	809	0.989	0.994	98.8875	0.12
4.807-5.878	0.198	26	0.142	656	0.144	688	0.981	0.99	99.1279	0.163
5.878-8.272	0.18	35	0.171	487	0.171	528	0.979	0.983	98.8636	0.196
8.272-59.086	0.155	11	0.196	288	0.194	300	0.982	0.979	99.6667	0.258

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