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- PDB-7nym: Mutant V517A - SH3 domain of JNK-interacting Protein 1 (JIP1) -

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Basic information

Entry
Database: PDB / ID: 7nym
TitleMutant V517A - 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
PHOSPHATE ION / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.614 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 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
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)
CCC: SH3 domain of JNK-interacting Protein 1 (JIP1)
DDD: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,22311
Polymers29,9934
Non-polymers1,2307
Water3,927218
1
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)15,8487
Polymers14,9972
Non-polymers8525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-34 kcal/mol
Surface area7280 Å2
MethodPISA
2
CCC: SH3 domain of JNK-interacting Protein 1 (JIP1)
DDD: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3754
Polymers14,9972
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-20 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.120, 84.254, 98.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 7498.314 Da / Num. of mol.: 4 / Mutation: V517A
Source method: isolated from a genetically manipulated source
Details: GHME 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: Needles
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: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2020
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.45→63.976 Å / Num. obs: 45428 / % possible obs: 94 % / Redundancy: 12.5 % / CC1/2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 1.454→1.518 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2272 / CC1/2: 0.46

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Processing

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

7nyk


Resolution: 1.614→63.976 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.629 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1976 1815 4.996 %
Rwork0.1314 34511 -
all0.135 --
obs-36326 99.967 %
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: 21.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.658 Å20 Å20 Å2
2--1.586 Å20 Å2
3----0.928 Å2
Refinement stepCycle: LAST / Resolution: 1.614→63.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 84 218 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132184
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171921
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6832948
X-RAY DIFFRACTIONr_angle_other_deg1.3731.6354434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4335240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.7621.438153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26715323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4821521
X-RAY DIFFRACTIONr_chiral_restr0.090.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_nbd_refined0.3180.2296
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2270.21766
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2929
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2138
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.211
X-RAY DIFFRACTIONr_nbd_other0.250.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.212
X-RAY DIFFRACTIONr_mcbond_it2.3811.775964
X-RAY DIFFRACTIONr_mcbond_other2.3781.769963
X-RAY DIFFRACTIONr_mcangle_it2.9222.6381192
X-RAY DIFFRACTIONr_mcangle_other2.9212.6421193
X-RAY DIFFRACTIONr_scbond_it5.5352.4561220
X-RAY DIFFRACTIONr_scbond_other5.5382.451216
X-RAY DIFFRACTIONr_scangle_it6.7613.4811752
X-RAY DIFFRACTIONr_scangle_other6.7613.4721747
X-RAY DIFFRACTIONr_lrange_it5.65222.0232264
X-RAY DIFFRACTIONr_lrange_other5.65322.052265
X-RAY DIFFRACTIONr_rigid_bond_restr2.84434105
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
1.614-1.6550.2341520.1625090.16426610.8950.9291000.154
1.655-1.7010.2251190.14324420.14725610.9160.9421000.135
1.701-1.750.2251300.14624010.1525310.9290.9441000.134
1.75-1.8040.2051150.14122820.14523970.9310.9431000.128
1.804-1.8630.2151060.1222610.12423670.9290.9591000.107
1.863-1.9280.1891050.10421910.10822960.9490.9691000.092
1.928-2.0010.2111170.10520960.11122130.9490.9711000.096
2.001-2.0830.1621070.10120440.10521510.9720.9771000.095
2.083-2.1750.172970.10119330.10420300.9640.9751000.097
2.175-2.2810.1911110.10518550.1119660.960.9731000.103
2.281-2.4040.1581000.09517830.09918830.9690.9791000.094
2.404-2.550.187780.09817120.10217900.9630.9781000.099
2.55-2.7260.193880.11415800.11816680.9530.9731000.116
2.726-2.9440.206660.12714850.1315520.9620.97299.93560.137
2.944-3.2240.207740.13113830.13514590.9530.97399.86290.145
3.224-3.6040.221700.14812590.15213290.9550.9691000.17
3.604-4.1590.183710.14111130.14411840.9620.9721000.172
4.159-5.0880.188390.1379550.1389940.9680.9791000.172
5.088-7.1730.233480.1967660.1988140.9530.9661000.24
7.173-63.9760.218220.2794610.2764920.9490.93398.17070.445

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