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- PDB-7nyl: Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1) -

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Basic information

Entry
Database: PDB / ID: 7nyl
TitleMutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)
ComponentsSH3 domain of JNK-interacting Protein 1 (JIP1)
KeywordsSIGNALING PROTEIN / SH3 domain of JNK-interacting protein 1 (JIP1)
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 / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / JNK cascade ...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 / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / JNK cascade / vesicle-mediated transport / mitochondrial membrane / positive regulation of JNK cascade / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / regulation of DNA-templated transcription / perinuclear region of cytoplasm / nucleus / plasma membrane / 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...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
trehalose / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPerez, L.M. / Ielasi, F.S. / Palencia, A. / Jensen, M.R.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)RC18114CC-NovoTarget France
Agence Nationale de la Recherche (ANR)MAPKAssembly France
CitationJournal: Nature / Year: 2022
Title: Visualizing protein breathing motions associated with aromatic ring flipping.
Authors: Marino Perez, L. / Ielasi, F.S. / Bessa, L.M. / Maurin, D. / Kragelj, J. / Blackledge, M. / Salvi, N. / Bouvignies, G. / Palencia, A. / Jensen, M.R.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: SH3 domain of JNK-interacting Protein 1 (JIP1)
BBB: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4554
Polymers14,9192
Non-polymers5372
Water86548
1
AAA: SH3 domain of JNK-interacting Protein 1 (JIP1)
BBB: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4554
Polymers14,9192
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area2290 Å2
ΔGint-1 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.055, 45.551, 46.006
Angle α, β, γ (deg.)90.000, 104.274, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / End auth comp-ID: THR / End label comp-ID: THR

Component-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLNGLNAAAA491 - 5485 - 62
2GLYGLYBBBB487 - 5481 - 62

NCS ensembles : (Details: r_ncsr_local_group_1s)

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Components

#1: Protein SH3 domain of JNK-interacting Protein 1 (JIP1) / 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 / C-Jun-amino-terminal kinase-interacting protein 1


Mass: 7459.299 Da / Num. of mol.: 2 / Mutation: H493A
Source method: isolated from a genetically manipulated source
Details: GHM belongs to expression vector pET28a / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP1, IB1, JIP1, PRKM8IP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQF2, phosphoinositide 5-phosphatase
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose /


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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 36.1 % / Description: neddles
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1-5% PEG 400, 2-2.5 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2020
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.93→45.55 Å / Num. obs: 8443 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 8.4 % / CC1/2: 0.99 / Net I/σ(I): 6.9
Reflection shellResolution: 1.93→2.03 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1083 / CC1/2: 0.66 / % possible all: 77.9

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NYK

7nyk


Resolution: 1.95→44.586 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.216 / SU ML: 0.249 / Cross valid method: FREE R-VALUE / ESU R: 0.225 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2545 403 4.849 %
Rwork0.2049 7908 -
all0.207 --
obs-8311 99.844 %
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: 31.846 Å2
Baniso -1Baniso -2Baniso -3
1-4.371 Å20 Å2-3.49 Å2
2---1.512 Å20 Å2
3----0.958 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 36 48 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131066
X-RAY DIFFRACTIONr_bond_other_d0.0010.017937
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6911448
X-RAY DIFFRACTIONr_angle_other_deg1.2331.5962164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2645118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69421.52872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22115156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1721510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.1840.2171
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.2936
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2469
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.29
X-RAY DIFFRACTIONr_nbd_other0.1790.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3070.29
X-RAY DIFFRACTIONr_mcbond_it2.4813.005478
X-RAY DIFFRACTIONr_mcbond_other2.4833.001477
X-RAY DIFFRACTIONr_mcangle_it3.7854.468594
X-RAY DIFFRACTIONr_mcangle_other3.7824.473595
X-RAY DIFFRACTIONr_scbond_it3.8223.617588
X-RAY DIFFRACTIONr_scbond_other3.8183.622589
X-RAY DIFFRACTIONr_scangle_it6.1045.219854
X-RAY DIFFRACTIONr_scangle_other6.15.224855
X-RAY DIFFRACTIONr_lrange_it8.13333.5671105
X-RAY DIFFRACTIONr_lrange_other8.1333.6081106
X-RAY DIFFRACTIONr_ncsr_local_group_10.140.051694
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
1.95-2.0010.33260.3296030.3296300.2760.30699.84130.319
2.001-2.0550.343220.3325750.3325970.3280.4271000.316
2.055-2.1150.294240.3085410.3075650.4380.5261000.287
2.115-2.180.349310.2995420.3015740.4620.59799.82580.27
2.18-2.2510.274300.2894960.2885260.7150.6951000.265
2.251-2.330.355240.2575160.2615410.750.76299.81520.233
2.33-2.4180.302240.2484750.255000.7030.7899.80.225
2.418-2.5160.258270.2474670.2474940.7890.8021000.225
2.516-2.6270.352170.2424400.2454570.6940.8221000.224
2.627-2.7550.338220.2064290.2124510.8020.8721000.187
2.755-2.9040.364220.1924090.2014310.8680.9061000.177
2.904-3.0790.289260.1643850.1714110.8840.9321000.151
3.079-3.290.206250.153620.1533890.9130.95199.48590.143
3.29-3.5520.266190.1693400.1753590.9520.951000.164
3.552-3.8890.196190.1462990.1493190.940.95999.68650.144
3.889-4.3440.112180.1362780.1352960.9780.9661000.138
4.344-5.0080.26140.1612550.1662730.9460.96398.53480.17
5.008-6.1140.24780.2072110.2092200.9510.93399.54550.212
6.114-8.5670.53220.1961790.1991810.9261000.203
8.567-44.5860.24730.2341050.2341090.8530.92499.08260.251

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