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- PDB-9ft9: Structure of the bipartite JNK1-JIP1 complex -

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Basic information

Entry
Database: PDB / ID: 9ft9
TitleStructure of the bipartite JNK1-JIP1 complex
Components
  • C-Jun-amino-terminal kinase-interacting protein 1
  • Isoform 1 of Mitogen-activated protein kinase 8
KeywordsSIGNALING PROTEIN / c-Jun N-terminal kinase 1 (JNK-1) Serine/threonine-protein kinase cell proliferation / differentiation / migration / transformation programmed cell death
Function / homology
Function and homology information


JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria / WNT5:FZD7-mediated leishmania damping / positive regulation of cyclase activity / histone deacetylase regulator activity ...JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria / WNT5:FZD7-mediated leishmania damping / positive regulation of cyclase activity / histone deacetylase regulator activity / NRAGE signals death through JNK / positive regulation of NLRP3 inflammasome complex assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / positive regulation of protein metabolic process / JUN kinase activity / mitogen-activated protein kinase / regulation of macroautophagy / response to UV / response to mechanical stimulus / stress-activated MAPK cascade / energy homeostasis / JNK cascade / protein serine/threonine kinase binding / negative regulation of protein binding / peptidyl-threonine phosphorylation / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to reactive oxygen species / FCERI mediated MAPK activation / regulation of circadian rhythm / histone deacetylase binding / cellular response to mechanical stimulus / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptidyl-serine phosphorylation / regulation of protein localization / cellular response to lipopolysaccharide / cellular response to oxidative stress / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / protein phosphorylation / positive regulation of apoptotic process / axon / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / negative regulation of apoptotic process / enzyme binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOrand, T. / Delaforge, E. / Palencia, A. / Jensen, M.R.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ScaffoldDisorder France
La ligue contre le cancerThibault Orand thesis funding France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Bipartite binding of the intrinsically disordered scaffold protein JIP1 to the kinase JNK1.
Authors: Orand, T. / Delaforge, E. / Lee, A. / Kragelj, J. / Tengo, M. / Tengo, L. / Blackledge, M. / Boeri Erba, E. / Davis, R.J. / Palencia, A. / Jensen, M.R.
History
DepositionJun 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Mitogen-activated protein kinase 8
B: C-Jun-amino-terminal kinase-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6373
Polymers46,1312
Non-polymers5061
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, isothermal titration calorimetry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.700, 137.700, 63.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Isoform 1 of Mitogen-activated protein kinase 8 / MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated ...MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 41634.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GAMA is from the expression vector / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P45983, mitogen-activated protein kinase
#2: Protein/peptide C-Jun-amino-terminal kinase-interacting protein 1


Mass: 4497.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GHM belong to the expression vector tag. This is a peptide of the intrinsically disorder scaffold protein JIP1. There is a deletion of the flexible linker comprising residues 176TLNNNSLGK184
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP1, IB1, JIP1, PRKM8IP / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.8 Å3/Da / Density % sol: 68 % / Description: rods
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% w/v PEG 3350, 0.1 M Bis Tris propane pH 6.5, 0.2 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2024
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.35→46.86 Å / Num. obs: 29338 / % possible obs: 99.9 % / Redundancy: 15.03 % / Biso Wilson estimate: 75.21 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 13.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 12.8 % / Num. unique obs: 2790 / CC1/2: 0.2 / Rrim(I) all: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDS2023data reduction
XSCALE2023data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.86 Å / SU ML: 0.5322 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.4863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: TLS refinement in phenix.refine B-factors are total (local + TLS + crystal)
RfactorNum. reflection% reflection
Rfree0.2701 1484 5.06 %
Rwork0.2313 27834 -
obs0.2336 29318 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.96 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 31 123 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923169
X-RAY DIFFRACTIONf_angle_d1.11534296
X-RAY DIFFRACTIONf_chiral_restr0.0572476
X-RAY DIFFRACTIONf_plane_restr0.0101544
X-RAY DIFFRACTIONf_dihedral_angle_d9.1905424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.45311170.4392489X-RAY DIFFRACTION99.2
2.43-2.510.54441130.44042546X-RAY DIFFRACTION100
2.51-2.610.44281310.3812502X-RAY DIFFRACTION99.96
2.61-2.730.36091290.32982508X-RAY DIFFRACTION100
2.73-2.880.33411540.30552509X-RAY DIFFRACTION100
2.88-3.060.33091170.30262542X-RAY DIFFRACTION100
3.06-3.290.33651540.28522489X-RAY DIFFRACTION99.96
3.29-3.620.34151260.24352550X-RAY DIFFRACTION100
3.62-4.150.3057970.20872559X-RAY DIFFRACTION99.74
4.15-5.220.22771790.19042524X-RAY DIFFRACTION100
5.22-46.860.21311670.19322616X-RAY DIFFRACTION99.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.460991807740.6766922349821.326254968442.040603541470.4476522469521.90972487592-0.2401942476640.2150386171570.251932882698-0.374618526740.1542860837190.0459752756868-0.2871272446180.4855458036452.75621418681E-50.672249026466-0.131288647611-0.04720419569060.7014619777160.0793685301930.635946223762-49.130066493465.8581690221-1.92393255282
21.857613827490.5297943291020.4099555261973.158699372781.364531085782.829069361880.0897347595386-0.0556678982186-0.4445379107640.2139970406440.138420016495-0.4436319263950.346955807540.5681605999248.90243137655E-50.5286657241490.0412941378676-0.05962905157630.7160932174760.04005077113490.730725815672-47.133382561538.972377565510.2567997155
31.118901991440.7004755429410.3080302601641.807435563550.07195744522660.124454139581-0.1607376085630.124070646315-0.231706286394-0.285836309550.02708636764130.5112305585850.282322427021-0.1085142092670.0004574552363230.6532881693010.0102274406245-0.1082272393860.6600489729-0.008054998345150.753202446564-60.303609754251.97026974132.32255584165
40.23567837823-0.1729465151970.02039573385140.3962028323340.190199737630.158053389691-0.444116854248-0.160433614249-0.2221559064050.706129671943-0.558778702604-0.5303906728560.02484171246570.518449180305-0.03049030342190.913340825534-0.146576562982-0.1908564629250.9695676545490.1496790827710.595501170605-44.350852678656.017966457825.9540955654
50.009522418533690.007709692394860.008119032591590.05653146282030.02647090151530.01458812638430.4341530291860.248181863693-0.361484139888-0.002014456437170.122419166431-0.00758104704852-0.2782116415890.09914573972550.0009467156556381.49465096162-0.2063193022480.2638246285691.22410455909-0.1178609437861.33554520626-42.158748933734.2644349341-9.24224762076
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 114 )AA7 - 1141 - 108
22chain 'A' and (resid 115 through 311 )AA115 - 311109 - 305
33chain 'A' and (resid 312 through 363 )AA312 - 363306 - 357
44chain 'B' and (resid 157 through 170 )BC157 - 1701 - 14
55chain 'B' and (resid 210 through 218 )BC210 - 21815 - 23

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