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- PDB-2fpd: Sad structure determination: crystal structure of the intrinsic d... -

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Basic information

Entry
Database: PDB / ID: 2fpd
TitleSad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein
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 / 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
trehalose / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0987
Polymers29,5644
Non-polymers5343
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-47 kcal/mol
Surface area12440 Å2
MethodPISA
2
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,19714
Polymers59,1288
Non-polymers1,0696
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14220 Å2
ΔGint-105 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.486, 114.486, 48.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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.: 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
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: AMMONIUM SULFATE, BICINE, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.967
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 2003
RadiationMonochromator: BENDABLE ASYMMETRICALLY CUT SI(111) CRYSTAL IN COMBINATION WITH VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 37925 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 8.02 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 7.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 8.24 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.28 / Rsym value: 0.34 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
CCP4model building
CNS1.1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→24.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1632143.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: EXPERIMENTAL PHASES WERE USED THROUGHOUT IN THE REFINEMENT, WHICH WAS BASED ON THE MLHL TARGET FUNCTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1947 5.1 %RANDOM
Rwork0.184 ---
obs0.184 37925 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.59 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.05→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 33 249 2382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.05→2.16 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.248 303 5.7 %
Rwork0.191 5051 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TRE_XPLOR_PARAM.TXTTRE_XPLOR_TOP.TXT

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