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- PDB-5qu7: Crystal Structure of swapped human Nck SH3.1 domain, 1.3A, orthor... -

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Basic information

Entry
Database: PDB / ID: 5qu7
TitleCrystal Structure of swapped human Nck SH3.1 domain, 1.3A, orthorhombic form III
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 / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cap-independent translational initiation / 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 / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cap-independent translational initiation / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / vesicle membrane / lamellipodium assembly / positive regulation of actin filament polymerization / RHOV GTPase cycle / negative regulation of PERK-mediated unfolded protein response / negative regulation of peptidyl-serine phosphorylation / protein kinase inhibitor activity / RHOU GTPase cycle / Generation of second messenger molecules / ephrin receptor signaling pathway / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell proliferation / signaling adaptor activity / antiviral innate immune response / negative regulation of insulin receptor signaling pathway / response to endoplasmic reticulum stress / ephrin receptor binding / regulation of cell migration / Downstream signal transduction / T cell activation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / molecular condensate scaffold activity / 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 / cell migration / signaling receptor complex adaptor activity / 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 / 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 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 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: 1.27 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
B: Cytoplasmic protein NCK1


Theoretical massNumber of molelcules
Total (without water)19,5342
Polymers19,5342
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-25 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.070, 48.870, 55.100
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 / NCK adaptor protein 1 / Nck-1 / SH2/SH3 adaptor protein NCK-alpha


Mass: 9766.842 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.38 Å3/Da / Density % sol: 10.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 8% tacsimate pH 5, 20% PEG 3350

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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: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.27→36.59 Å / Num. obs: 28241 / % possible obs: 96.5 % / Redundancy: 6.34 % / Biso Wilson estimate: 27.941 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.075 / Χ2: 0.848 / Net I/σ(I): 9.49 / Num. measured all: 178907 / Scaling rejects: 11
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
1.27-1.32.9473.4250.254483211015214.16972.1
1.3-1.343.2712.3720.395846210417872.81884.90.222
1.34-1.383.7452.0910.567172200419152.42895.60.325
1.38-1.425.1321.5830.889925196619341.76198.40.561
1.42-1.477.1571.321.413549189318931.4241000.678
1.47-1.527.1760.8882.1213219184318420.95899.90.861
1.52-1.587.3210.6832.8113134179417940.7361000.917
1.58-1.646.8860.4883.7511788171217120.5281000.936
1.64-1.717.640.3465.3812652165716560.37199.90.969
1.71-1.87.4910.2437.4111866158415840.2611000.983
1.8-1.897.090.14710.7310713151115110.1591000.993
1.89-2.017.180.10414.4610304143614350.11299.90.997
2.01-2.157.4650.08219.019988133813380.0881000.997
2.15-2.327.3410.07221.69353127412740.0771000.997
2.32-2.546.8410.06522.578106118511850.0711000.997
2.54-2.847.50.05826.597898105310530.0631000.998
2.84-3.287.0950.05528.1367479539510.0699.80.998
3.28-4.026.5460.05329.0353618208190.05899.90.993
4.02-5.686.9390.05330.3844696456440.05899.80.996
5.68-36.595.9390.05627.3723343953930.06299.50.996

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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: 1.27→36.59 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.6 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1081 5.1 %RANDOM
Rwork0.1714 ---
obs0.1738 19981 71.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.41 Å2 / Biso mean: 20.977 Å2 / Biso min: 10.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å2-0 Å2
2---0.1 Å20 Å2
3---1.48 Å2
Refinement stepCycle: final / Resolution: 1.27→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 0 105 1075
Biso mean---34.51 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131040
X-RAY DIFFRACTIONr_bond_other_d0.0060.018974
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.6481410
X-RAY DIFFRACTIONr_angle_other_deg1.2851.5982258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6485123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60821.38972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7551512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_rigid_bond_restr1.69432014
LS refinement shellResolution: 1.269→1.302 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.696 7 -
Rwork0.353 70 -
all-77 -
obs--3.66 %

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