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- PDB-2ci8: sh2 domain of human nck1 adaptor protein - uncomplexed -

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Basic information

Entry
Database: PDB / ID: 2ci8
Titlesh2 domain of human nck1 adaptor protein - uncomplexed
ComponentsCYTOPLASMIC PROTEIN NCK1
KeywordsTRANSLATION / BINDING SPECIFICITY / HOST-PATHOGEN / INTERACTIONS
Function / homology
Function and homology information


positive regulation of cap-dependent translational initiation / regulation of translation initiation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / positive regulation of translation in response to endoplasmic reticulum stress / protein phosphatase type 1 complex / 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 / signal complex assembly ...positive regulation of cap-dependent translational initiation / regulation of translation initiation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / positive regulation of translation in response to endoplasmic reticulum stress / protein phosphatase type 1 complex / 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 / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / vesicle membrane / lamellipodium assembly / positive regulation of actin filament polymerization / negative regulation of T cell receptor signaling pathway / RHOV GTPase cycle / protein kinase inhibitor activity / negative regulation of PERK-mediated unfolded protein response / 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 / ephrin receptor binding / antiviral innate immune response / negative regulation of insulin receptor signaling pathway / Downstream signal transduction / protein sequestering activity / response to endoplasmic reticulum stress / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / T cell activation / regulation of cell migration / actin filament organization / FCGR3A-mediated phagocytosis / molecular condensate scaffold activity / PKR-mediated signaling / positive regulation of neuron projection development / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / 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 / : / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / : / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFrese, S. / Schubert, W.-D. / Findeis, A.C. / Marquardt, T. / Roske, Y.S. / Stradal, T.E.B. / Heinz, D.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Phosphotyrosine Peptide Binding Specificity of Nck1 and Nck2 Src Homology 2 Domains.
Authors: Frese, S. / Schubert, W.-D. / Findeis, A.C. / Marquardt, T. / Roske, Y.S. / Stradal, T.E.B. / Heinz, D.W.
History
DepositionMar 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_caveat / database_PDB_rev ...database_PDB_caveat / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / pdbx_database_proc / pdbx_database_status / struct_conn / struct_conn_type
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOPLASMIC PROTEIN NCK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1376
Polymers11,5141
Non-polymers6235
Water1,20767
1
A: CYTOPLASMIC PROTEIN NCK1
hetero molecules

A: CYTOPLASMIC PROTEIN NCK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,27312
Polymers23,0282
Non-polymers1,24510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area5820 Å2
ΔGint-122.6 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.854, 82.484, 44.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

DetailsTHE DIMER IS A STRAND EXCHANGE DIMER AND MAYNOT HAVE BIOLOGICAL SIGNIFICANCE.

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Components

#1: Protein CYTOPLASMIC PROTEIN NCK1 / NCK ADAPTOR PROTEIN 1 / SH2/SH3 ADAPTOR PROTEIN NCK-ALPHA


Mass: 11514.019 Da / Num. of mol.: 1 / Fragment: SH2-DOMAIN, RESIDUES 281-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 (AMERSHAM BIOSCIENCES) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P16333
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.46 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: METHOD: HANGING-DROP, VAPOR-DIFFUSION AT 4 DEGREES C, PROTEIN: 8 MG/ML PROTEIN IN 20 MM TRIS/HCL, PH 8.0, RESERVOIR: 25% PEG5000 MME, 0.1M MES PH 6.5, 0.2M (NH4)2SO4, 0.1M GUANIDINE HCL. CRYOPROTECTANT: 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91977
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91977 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 11119 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JYU

1jyu


Resolution: 1.8→30.26 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.556 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 526 4.8 %RANDOM
Rwork0.23 ---
obs0.232 10457 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 35 67 907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021981
X-RAY DIFFRACTIONr_bond_other_d0.0050.02687
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9641314
X-RAY DIFFRACTIONr_angle_other_deg3.30531695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95624.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16615192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.242155
X-RAY DIFFRACTIONr_chiral_restr0.3930.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021053
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02203
X-RAY DIFFRACTIONr_nbd_refined0.2080.3167
X-RAY DIFFRACTIONr_nbd_other0.180.3650
X-RAY DIFFRACTIONr_nbtor_refined0.20.5428
X-RAY DIFFRACTIONr_nbtor_other0.1510.5506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.5101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.331
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 27 -
Rwork0.269 753 -
obs--97.26 %
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)
14.0118-1.3953-0.45232.823-0.14071.48290.1874-0.26110.0433-0.1859-0.063-0.0907-0.06120.0319-0.12430.0385-0.00260.0016-0.05940.0193-0.115612.64334.51714.921
25.20341.89610.45493.22030.37831.71170.4226-0.38380.19830.6789-0.3160.69580.0749-0.217-0.10650.125-0.07050.073-0.1096-0.0303-0.122642.74229.9137.992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A280 - 333
2X-RAY DIFFRACTION2A334 - 377

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