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- PDB-2fpf: Crystal structure of the ib1 sh3 dimer at low resolution -

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Basic information

Entry
Database: PDB / ID: 2fpf
TitleCrystal structure of the ib1 sh3 dimer at low resolution
ComponentsC-jun-amino-terminal kinase interacting protein 1
KeywordsSIGNALING PROTEIN / SCAFFOLD PROTEIN 1 / ISLET-BRAIN-1 / IB-1 / MITOGEN-ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 1 / JIP-1 RELATED PROTEIN / JRP
Function / homology
Function and homology information


dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / regulation of JNK cascade / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / negative regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway ...dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / regulation of JNK cascade / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / negative regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / dendritic growth cone / kinesin binding / axonal growth cone / vesicle-mediated transport / JNK cascade / positive regulation of JNK cascade / mitochondrial membrane / neuron projection / axon / neuronal cell body / synapse / dendrite / regulation of DNA-templated transcription / endoplasmic reticulum membrane / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / SH3 Domains / SH3 type barrels. / Src homology 3 domains ...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 / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKristensen, O. / Dar, I. / Gajhede, M.
Citation
#1: Journal: Science / Year: 1997
Title: A cytoplasmic inhibitor of the JNK signal transduction pathway
Authors: Dickens, M. / Rogers, J.S. / Cavanagh, J. / Raitano, A. / Xia, Z. / Halpern, J.R. / Greenberg, M.E. / Sawyers, C.L. / Davis, R.J.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: IB1, a JIP-1-related nuclear protein present in insulin-secreting cells
Authors: Bonny, C. / Nicod, P. / Waeber, G.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: Recruitment of JNK to JIP1 and JNK-dependent JIP1 phosphorylation regulates JNK module dynamics and activation
Authors: Nihalani, D. / Wong, H.N. / Holzman, L.B.
#4: Journal: Mol.Cell.Biol. / Year: 1999
Title: The JIP group of mitogen-activated protein kinase scaffold proteins
Authors: Yasuda, J. / Whitmarsh, A.J. / Cavanagh, J. / Sharma, M. / Davis, R.J.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1


Theoretical massNumber of molelcules
Total (without water)33,8534
Polymers33,8534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.868, 57.000, 145.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.45925, -0.42769, 0.77857), (-0.43943, -0.87109, -0.21931), (0.772, -0.24141, -0.58799)-134.52009, 5.49, 256.50337
3given(-0.57065, 0.81133, 0.12688), (0.53193, 0.48291, -0.69559), (-0.62563, -0.32945, -0.70714)8.70527, 107.03895, 284.67057
4given(-0.4872, -0.5057, -0.71197), (-0.51472, -0.49233, 0.70191), (-0.70548, 0.70844, -0.02043)124.15242, -137.62102, 189.48617

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Components

#1: Protein
C-jun-amino-terminal kinase interacting protein 1 / JNK-interacting protein 1 / JIP-1 / JNK MAP kinase scaffold protein 1 / Islet-brain-1 / IB-1 / ...JNK-interacting protein 1 / JIP-1 / JNK MAP kinase scaffold protein 1 / Islet-brain-1 / IB-1 / Mitogen-activated protein kinase 8-interacting protein 1 / JIP-1-related protein / JRP


Mass: 8463.264 Da / Num. of mol.: 4 / Fragment: SH3 DOMAIN, RESIDUES -1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk8ip1, Ib1, Jip1 / Plasmid: PGEX 4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA BL21(DE3)PLYSS / References: UniProt: Q9R237

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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: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SODIUM CITRATE, HEPES, HYDROGEN PEROXIDE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 8075 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 12.07
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.461 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FPD

2fpd


Resolution: 3→28.77 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 230208.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 572 7.4 %RANDOM
Rwork0.224 ---
obs0.224 7679 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.58 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å20 Å20 Å2
2--8.73 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 0 0 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.691.5
X-RAY DIFFRACTIONc_mcangle_it10.392
X-RAY DIFFRACTIONc_scbond_it14.422
X-RAY DIFFRACTIONc_scangle_it20.592.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 88 7.4 %
Rwork0.288 1094 -
obs--89 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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