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- PDB-5qua: Crystal Structure of swapped human Nck SH3.1 domain, 1.5A, C2221 -

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Basic information

Entry
Database: PDB / ID: 5qua
TitleCrystal Structure of swapped human Nck SH3.1 domain, 1.5A, C2221
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 / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity ...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 / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / 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 / protein kinase inhibitor activity / negative regulation of PERK-mediated unfolded protein response / 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 / regulation of cell migration / negative regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / response to endoplasmic reticulum stress / ephrin receptor binding / molecular condensate scaffold activity / T cell activation / Downstream signal transduction / 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 / positive regulation of neuron projection development / VEGFA-VEGFR2 Pathway / cell migration / cell-cell junction / 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 / 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 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: 1.51 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 1.1Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2May 12, 2021Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_type
Revision 1.3Jun 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 1.4Mar 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 1.5Apr 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,5992
Polymers20,5992
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-24 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.600, 85.190, 56.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 10299.410 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 / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.56 Å3/Da / Density % sol: 21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris/HCl pH 6.5, 2 M ammonium sulfate

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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: 1.5→35.32 Å / Num. obs: 20939 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 47.855 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.029 / Χ2: 0.827 / Net I/σ(I): 21.87 / Num. measured all: 134090 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. possibleNum. unique obs% possible allRmerge(I) obsCC1/2Rrim(I) all
1.5-1.546.5050.1497381535149797.5
1.54-1.586.3870.394841486148599.97.2090.1687.854
1.58-1.636.0230.3487401460145199.47.4420.2848.154
1.63-1.686.5990.7693241414141399.92.7690.4153.007
1.68-1.736.6731.279102136413641001.6620.6441.804
1.73-1.796.5571.958728133113311001.1020.811.197
1.79-1.866.4323.2981751272127199.90.620.9430.675
1.86-1.946.0525.7175291246124499.80.3440.970.377
1.94-2.026.62510.2677911177117699.90.1860.9910.202
2.02-2.126.68914.887505112211221000.1230.9960.133
2.12-2.246.60520.8972261095109499.90.0840.9980.091
2.24-2.376.39929.4365851030102999.90.0540.9990.059
2.37-2.546.08836.68586996596499.90.040.9990.044
2.54-2.746.77449.94608389989899.90.0310.9990.033
2.74-36.55762.4355418458451000.0240.9990.027
3-3.356.13274.23470977076899.70.0210.022
3.35-3.875.87178.83396967767699.90.01710.019
3.87-4.746.589.82377058158099.80.01510.017
4.74-6.715.84986.45267346045799.30.01610.018
6.71-35.325.65385.24154928227497.20.0170.9990.019

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.51→35.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.959 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 706 4.6 %RANDOM
Rwork0.2001 ---
obs0.2014 14743 75.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.15 Å2 / Biso mean: 45.595 Å2 / Biso min: 23.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0 Å2
2---0.57 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.51→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 0 61 1014
Biso mean---42.74 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013977
X-RAY DIFFRACTIONr_bond_other_d0.0010.018903
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.6371321
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5952091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9135112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72222.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69815183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.163158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
LS refinement shellResolution: 1.515→1.554 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 2 -
Rwork0.446 55 -
all-57 -
obs--3.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2003-1.14573.01778.77740.58098.77480.28510.3301-0.5182-1.2250.10480.20490.2980.1307-0.38990.24760.0014-0.05020.0505-0.00930.0577-8.779-34.040.648
227.876-18.60484.743921.9897-3.88315.42970.0871-0.4841.1360.8178-0.4779-0.8726-1.1585-0.42050.39080.36230.0333-0.04980.1549-0.03830.062-10.621-21.77611.358
38.3067-0.68643.73555.8336-4.36168.79240.2384-0.2312-1.0467-0.25480.01420.70450.3199-0.9795-0.25270.0671-0.0034-0.0450.1911-0.10490.2972-13.009-32.8474.959
49.5543.3191-1.489515.1787-10.95397.99870.54641.1089-0.4226-1.90330.00570.64471.47790.0992-0.55210.49610.109-0.19830.1665-0.11750.181-15.641-26.45-7.723
51.8741-0.31930.48836.32221.78433.09830.1071-0.0356-0.00020.1659-0.0779-0.210.29570.2733-0.02920.04040.03510.00870.10740.01740.0275-12.98-11.683-2.04
612.02651.134512.657611.5661-6.20518.10350.03410.3155-0.7149-0.1363-0.2992-1.64160.10220.5430.26510.04180.00820.04320.23980.010.3009-4.804-6.611-2.091
72.42310.79761.11196.28071.45465.01570.0043-0.0776-0.0387-0.2361-0.13990.16170.0006-0.18970.13560.02240.02820.00140.12-0.02430.0308-17.789-9.612-4.729
84.68291.5893-3.481922.77357.83866.24920.1015-0.6256-0.22960.14040.0876-0.9837-0.0410.5826-0.18910.10720.058-0.08020.19940.04940.1917-4.652-16.4430.284
99.14811.42271.17214.9288-4.49976.0899-0.0083-0.2728-0.3707-1.3619-0.2621.1454-0.1498-0.57770.27040.2040.1081-0.19790.1218-0.08740.2335-14.962-26.68-1.45
105.5015-4.24750.56137.5283-1.97167.04750.07120.2456-0.6967-0.4898-0.22020.6670.3917-0.38490.1490.13010.015-0.03070.1017-0.04580.1468-12.79-30.9131.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 11
2X-RAY DIFFRACTION2A12 - 16
3X-RAY DIFFRACTION3A17 - 28
4X-RAY DIFFRACTION4A29 - 35
5X-RAY DIFFRACTION5A36 - 56
6X-RAY DIFFRACTION6B0 - 6
7X-RAY DIFFRACTION7B7 - 29
8X-RAY DIFFRACTION8B30 - 35
9X-RAY DIFFRACTION9B36 - 40
10X-RAY DIFFRACTION10B41 - 57

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