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- PDB-5qu5: Domain Swap in the first SH3 domain of human Nck1 -

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Basic information

Entry
Database: PDB / ID: 5qu5
TitleDomain Swap in the first SH3 domain of human Nck1
ComponentsCytoplasmic protein NCK1Cytoplasm
KeywordsSIGNALING PROTEIN / SH3 DOMAIN / ADAPTOR / PEPTIDE BINDING / DOMAIN SWAP
Function / homology
Function and homology information


positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension ...positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / vesicle membrane / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / protein kinase inhibitor activity / antiviral innate immune response / RHOU GTPase cycle / Generation of second messenger molecules / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / signaling adaptor activity / negative regulation of peptidyl-serine phosphorylation / positive regulation of T cell proliferation / regulation of cell migration / T cell activation / negative regulation of insulin receptor signaling pathway / response to endoplasmic reticulum stress / ephrin receptor binding / Downstream signal transduction / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / molecular condensate scaffold activity / actin filament organization / FCGR3A-mediated phagocytosis / PKR-mediated signaling / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / cell-cell junction / signaling receptor complex adaptor activity / cell migration / protein-macromolecule adaptor activity / Potential therapeutics for SARS / ribosome / cadherin binding / protein domain specific binding / signaling receptor binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsBurger, D. / Ruf, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Small molecule AX-024 reduces T cell proliferation independently of CD3ε/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain.
Authors: Richter, K. / Rufer, A.C. / Muller, M. / Burger, D. / Casagrande, F. / Grossenbacher, T. / Huber, S. / Hug, M.N. / Koldewey, P. / D'Osualdo, A. / Schlatter, D. / Stoll, T. / Rudolph, M.G.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_type
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Database references / Refinement description / Category: citation / pdbx_initial_refinement_model / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic protein NCK1
B: Cytoplasmic protein NCK1


Theoretical massNumber of molelcules
Total (without water)23,7382
Polymers23,7382
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-22 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.200, 55.170, 55.230
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 Cytoplasmic protein NCK1 / Cytoplasm / NCK adaptor protein 1 / Nck-1 / SH2/SH3 adaptor protein NCK-alpha


Mass: 11869.125 Da / Num. of mol.: 2 / Fragment: SH3 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK1, NCK / Plasmid: PET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16333
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 5-20 mg/mL protein in 25mM HEPES\/NaOH pH7.8, 150mM NaCl mixed 60-70% with 40-30% reservoir consisting of 0.1M Bis-Tris/HCl pH5.5, 2M NaCl, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.1→39.03 Å / Num. obs: 48767 / % possible obs: 96.4 % / Redundancy: 7.215 % / Biso Wilson estimate: 21.685 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Χ2: 0.757 / Net I/σ(I): 8.16 / Num. measured all: 351842 / Scaling rejects: 138
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
1.1-1.137.10113.6610.1241153682339614.73492.2
1.13-1.167.0836.4540.2923928359833786.95993.90.163
1.16-1.197.4935.1920.4124630347932875.57394.50.353
1.19-1.237.3444.4660.5123808341532424.80394.90.321
1.23-1.277.0443.4120.722279331331633.68595.50.356
1.27-1.317.0622.610.9421745321230792.81895.90.492
1.31-1.367.5542.1241.3322283307029502.28196.10.62
1.36-1.427.4871.481221622299928881.59296.30.801
1.42-1.487.3491.022.8420261284427571.09996.90.877
1.48-1.566.8140.6753.9218078272526530.73297.40.921
1.56-1.647.4610.4395.9219161261325680.47398.30.971
1.64-1.747.6290.3027.8718570249124340.32497.70.985
1.74-1.867.4730.18511.3617158233122960.19998.50.993
1.86-2.017.1160.1116.6615334218721550.11998.50.996
2.01-2.26.5450.07321.5813011201319880.0898.80.997
2.2-2.467.4380.05927.4613359182117960.06498.60.998
2.46-2.847.2710.0531.111736163216140.05498.90.999
2.84-3.486.7950.03836.659424139913870.04199.10.999
3.48-4.926.3850.03140.256979110610930.03398.80.999
4.92-39.036.7820.02941.6543616486430.03199.21

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.11→39.03 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.907 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1391 4.9 %RANDOM
Rwork0.1523 ---
obs0.1551 26973 57.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.07 Å2 / Biso mean: 20.141 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0 Å2
2--0.22 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 1.11→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 7 160 1171
Biso mean--29.65 31.94 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021070
X-RAY DIFFRACTIONr_bond_other_d0.0040.02985
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9311447
X-RAY DIFFRACTIONr_angle_other_deg1.08432292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38724.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32115208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.293159
X-RAY DIFFRACTIONr_chiral_restr0.150.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021181
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02228
X-RAY DIFFRACTIONr_rigid_bond_restr3.71732055
X-RAY DIFFRACTIONr_sphericity_free25.6375112
X-RAY DIFFRACTIONr_sphericity_bonded12.2152081
LS refinement shellResolution: 1.107→1.136 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.385 33 -
Rfree-0 -
obs--0.91 %

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