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- PDB-5qu8: Crystal Structure of symmetric swapped human Nck SH3.1 domain, 0.... -

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Basic information

Entry
Database: PDB / ID: 5qu8
TitleCrystal Structure of symmetric swapped human Nck SH3.1 domain, 0.93A, orthorhombic form IV
ComponentsCytoplasmic protein NCK1
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 / negative regulation of peptidyl-serine phosphorylation / 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 / positive regulation of T cell proliferation / regulation of cell migration / T cell activation / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / response to endoplasmic reticulum stress / Downstream signal transduction / molecular condensate scaffold activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / cytoplasm / cytosol
Similarity search - Function
Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsRudolph, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3222
Polymers10,2991
Non-polymers231
Water1,13563
1
A: Cytoplasmic protein NCK1
hetero molecules

A: Cytoplasmic protein NCK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6454
Polymers20,5992
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4780 Å2
ΔGint-45 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.100, 55.170, 27.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cytoplasmic protein NCK1 / NCK adaptor protein 1 / Nck-1 / SH2/SH3 adaptor protein NCK-alpha


Mass: 10299.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK1, NCK / Plasmid: PET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16333
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.45 Å3/Da / Density % sol: 15.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 0.93→27.6 Å / Num. obs: 36162 / % possible obs: 88.1 % / Redundancy: 5.45 % / Biso Wilson estimate: 17.679 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.072 / Χ2: 0.846 / Net I/σ(I): 6.8 / Num. measured all: 196914 / Scaling rejects: 265
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
0.93-1.063.53914.7790.172948613109833217.33163.6
1.06-1.095.9363.4780.5912922218721773.81499.50.588
1.09-1.155.7941.8771.0321676375637412.06399.60.803
1.15-1.256.1590.8882.0529225475847450.9799.70.926
1.25-1.396.120.4963.3828147461345990.54299.70.972
1.39-1.576.0710.2316.8222850377037640.25399.80.989
1.57-1.866.4620.10114.0522204343634360.1111000.995
1.86-2.45.6270.05723.2415822282028120.06399.70.997
2.4-4.165.6670.04328.711436203420180.04899.20.998
4.16-27.65.8480.03230.9331465435380.03599.10.999

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 0.93→27.6 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.531 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 961 4.9 %RANDOM
Rwork0.1489 ---
obs0.1506 18459 47.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.66 Å2 / Biso mean: 17.542 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å2-0 Å2
2---1.77 Å20 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 0.93→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms493 0 1 63 557
Biso mean--25.15 32.42 -
Num. residues----58
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013552
X-RAY DIFFRACTIONr_bond_other_d0.0020.018514
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.65756
X-RAY DIFFRACTIONr_angle_other_deg1.441.5931199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.621569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76122.05139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15915109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.824156
X-RAY DIFFRACTIONr_chiral_restr0.1010.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_rigid_bond_restr5.89231066
LS refinement shellResolution: 0.93→0.954 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.781 1 -
Rwork0.48 24 -
all-25 -
obs--0.84 %

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