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- PDB-2fpe: Conserved dimerization of the ib1 src-homology 3 domain -

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Basic information

Entry
Database: PDB / ID: 2fpe
TitleConserved dimerization of the ib1 src-homology 3 domain
ComponentsC-jun-amino-terminal kinase interacting protein 1
KeywordsSIGNALING PROTEIN / SRC-HOMOLOGY 3 (SH3) DOMAIN / ALL BETA STRUCTURE
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 / negative regulation of JNK cascade / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / dendritic growth cone / kinesin binding ...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 / negative regulation of JNK cascade / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / dendritic growth cone / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / axonal growth cone / JNK cascade / vesicle-mediated transport / mitochondrial membrane / positive regulation of JNK cascade / neuron projection / axon / dendrite / neuronal cell body / synapse / endoplasmic reticulum membrane / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / signal transduction / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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 / Src homology 3 domains / SH3 type barrels. ...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 / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
SULFUR DIOXIDE / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGuenat, S. / Dar, I. / Bonny, C. / Kastrup, J.S. / Gajhede, M. / Kristensen, O.
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 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71119
Polymers59,1288
Non-polymers1,58311
Water10,755597
1
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3536
Polymers14,7822
Non-polymers5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-42 kcal/mol
Surface area7380 Å2
MethodPISA
2
C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1604
Polymers14,7822
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-22 kcal/mol
Surface area7250 Å2
MethodPISA
3
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0385
Polymers14,7822
Non-polymers2563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-18 kcal/mol
Surface area6520 Å2
MethodPISA
4
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1604
Polymers14,7822
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-23 kcal/mol
Surface area6970 Å2
MethodPISA
5
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,42338
Polymers118,25616
Non-polymers3,16722
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_546-x+1/2,y-1/2,-z+11
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area29020 Å2
ΔGint-284 kcal/mol
Surface area44360 Å2
MethodPISA
6
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,42338
Polymers118,25616
Non-polymers3,16722
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_646-x+3/2,y-1/2,-z+11
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area28140 Å2
ΔGint-277 kcal/mol
Surface area44910 Å2
MethodPISA
7
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71119
Polymers59,1288
Non-polymers1,58311
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area13660 Å2
ΔGint-137 kcal/mol
Surface area22870 Å2
MethodPISA
8
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

G: C-jun-amino-terminal kinase interacting protein 1
H: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

E: C-jun-amino-terminal kinase interacting protein 1
F: C-jun-amino-terminal kinase interacting protein 1
hetero molecules

C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71119
Polymers59,1288
Non-polymers1,58311
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+3/2,y+1/2,-z+11
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area11100 Å2
ΔGint-132 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.594, 81.591, 89.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11F-805-

SO2

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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: 7390.998 Da / Num. of mol.: 8 / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-SO2 / SULFUR DIOXIDE / Sulfur dioxide


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.4 Å3/Da / Density % sol: 47 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: AMMONIUM SULFATE, BICINE, PEG 400, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 99813 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 20.8
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.324 / % possible all: 88.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
CNSrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FPD

2fpd


Resolution: 1.75→19.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1129777.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANOMALOUS DATA WAS USED IN THE REFINEMENT. THE FRIEDEL PAIRS WEW USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2056 2.1 %RANDOM
Rwork0.204 ---
obs0.204 99813 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.62 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å20 Å20 Å2
2--11.77 Å20 Å2
3----8.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 95 597 4879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 268 1.8 %
Rwork0.292 14455 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SO4_XPLOR_PARAM.TXTSO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION415P.PARAM15P.TOP
X-RAY DIFFRACTION5SO2.PARAMSO2.TOP

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