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

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Basic information

Entry
Database: PDB / ID: 8rpp
TitleCrystal 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
KeywordsSIGNALING 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 ...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 / regulation of NMDA receptor activity / mating behavior / dendrite morphogenesis / protein kinase activator activity / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / social behavior / negative regulation of apoptotic signaling pathway / behavioral fear response / negative regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport / JNK cascade / regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / positive regulation of JNK cascade / mitochondrial membrane / MAPK cascade / amyloid-beta binding / postsynaptic density / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / regulation of DNA-templated transcription / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / structural molecule activity / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
JIP2, SH3 domain / JIP1, SH3 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...JIP2, SH3 domain / JIP1, SH3 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
C-Jun-amino-terminal kinase-interacting protein 2 / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.867 Å
AuthorsPalencia, A. / Marino-Perez, L. / Ielasi, F.I. / Jensen, M.R.
Funding support France, 5items
OrganizationGrant numberCountry
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
CitationJournal: Structure / Year: 2024
Title: Structural basis of homodimerization of the JNK scaffold protein JIP2 and its heterodimerization with JIP1.
Authors: Marino Perez, L. / Ielasi, F.S. / Lee, A. / Delaforge, E. / Juyoux, P. / Tengo, M. / Davis, R.J. / Palencia, A. / Jensen, M.R.
History
DepositionJan 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5364
Polymers29,5364
Non-polymers00
Water3,279182
1
A: C-Jun-amino-terminal kinase-interacting protein 2
D: C-Jun-amino-terminal kinase-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)14,7092
Polymers14,7092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-9 kcal/mol
Surface area6190 Å2
MethodPISA
2
B: C-Jun-amino-terminal kinase-interacting protein 2
C: C-Jun-amino-terminal kinase-interacting protein 2


Theoretical massNumber of molelcules
Total (without water)14,8262
Polymers14,8262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-9 kcal/mol
Surface area6910 Å2
MethodPISA
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 number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

21B-756-

HOH

31B-757-

HOH

41D-637-

HOH

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Components

#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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Malonate 1.5 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2021
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.867→59.086 Å / Num. obs: 25670 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.062 / Rrim(I) all: 0.098 / Net I/σ(I): 10.8
Reflection shellResolution: 1.867→1.899 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1340 / CC1/2: 0.76 / Rpim(I) all: 0.332 / Rrim(I) all: 0.644 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
AutoProcess1.1.7data reduction
STARANISO2.3.73data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.867→59.086 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.1936 1283 4.999 %
Rwork0.1482 24380 -
all0.15 --
obs-25663 99.577 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.255 Å20.128 Å2-0 Å2
2--0.255 Å20 Å2
3----0.828 Å2
Refinement stepCycle: LAST / Resolution: 1.867→59.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 0 182 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122141
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161819
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6512915
X-RAY DIFFRACTIONr_angle_other_deg0.5251.5534226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8965249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.0221027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72910312
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.80110137
X-RAY DIFFRACTIONr_chiral_restr0.0660.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_nbd_refined0.2220.2367
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21847
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21020
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2149
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3450.219
X-RAY DIFFRACTIONr_nbd_other0.1640.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.228
X-RAY DIFFRACTIONr_mcbond_it2.0962.382984
X-RAY DIFFRACTIONr_mcbond_other2.0962.382984
X-RAY DIFFRACTIONr_mcangle_it3.0713.5491228
X-RAY DIFFRACTIONr_mcangle_other3.073.5521229
X-RAY DIFFRACTIONr_scbond_it3.4782.7631157
X-RAY DIFFRACTIONr_scbond_other3.4762.7641158
X-RAY DIFFRACTIONr_scangle_it5.3924.0061684
X-RAY DIFFRACTIONr_scangle_other5.394.0071685
X-RAY DIFFRACTIONr_lrange_it6.93137.1282395
X-RAY DIFFRACTIONr_lrange_other6.90536.1442370
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.867-1.9160.304930.21118300.21519280.9440.96999.74070.2
1.916-1.9680.206760.19517840.19618650.9730.97699.73190.184
1.968-2.0250.246780.18517050.18817840.9670.97899.94390.172
2.025-2.0870.255570.16916990.17217650.9620.98299.49010.158
2.087-2.1560.2131000.16516080.16817150.970.98399.59180.15
2.156-2.2310.1771260.15414840.15616170.980.98399.56710.141
2.231-2.3150.212940.14914840.15315830.9740.98699.68410.137
2.315-2.410.213690.16514560.16715310.9740.98499.60810.151
2.41-2.5170.229880.15913570.16314550.9710.98599.31270.146
2.517-2.6390.236490.15413600.15714150.9630.98599.5760.145
2.639-2.7820.226630.14912360.15313030.9720.98699.6930.143
2.782-2.950.195810.1511890.15312740.9780.98699.6860.147
2.95-3.1530.204650.14811080.15111770.9750.98799.66010.148
3.153-3.4050.207490.13910640.14111140.9780.98999.91020.142
3.405-3.7290.147420.1279630.12810080.9910.99199.70240.138
3.729-4.1670.136280.1128750.1139130.9920.99398.90470.129
4.167-4.8070.141530.1017470.1038090.9890.99498.88750.12
4.807-5.8780.198260.1426560.1446880.9810.9999.12790.163
5.878-8.2720.18350.1714870.1715280.9790.98398.86360.196
8.272-59.0860.155110.1962880.1943000.9820.97999.66670.258

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