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- PDB-2cia: human nck2 sh2-domain in complex with a decaphosphopeptide from t... -

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Basic information

Entry
Database: PDB / ID: 2cia
Titlehuman nck2 sh2-domain in complex with a decaphosphopeptide from translocated intimin receptor (tir) of epec
Components
  • CYTOPLASMIC PROTEIN NCK2
  • TRANSLOCATED INTIMIN RECEPTOR
KeywordsSH2-DOMAIN / SH3 DOMAIN / PHOSPHORYLATION / BINDING SPECIFICITY
Function / homology
Function and homology information


Regulation of cortical dendrite branching / regulation of translation initiation in response to endoplasmic reticulum stress / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / cytoskeletal anchor activity / signal complex assembly / Activation of RAC1 / Nephrin family interactions ...Regulation of cortical dendrite branching / regulation of translation initiation in response to endoplasmic reticulum stress / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / cytoskeletal anchor activity / signal complex assembly / Activation of RAC1 / Nephrin family interactions / vesicle membrane / Ephrin signaling / lamellipodium assembly / positive regulation of actin filament polymerization / RHOV GTPase cycle / negative regulation of PERK-mediated unfolded protein response / RHOU GTPase cycle / ephrin receptor signaling pathway / positive regulation of T cell proliferation / signaling adaptor activity / phosphotyrosine residue binding / Downstream signal transduction / SH2 domain binding / T cell activation / actin filament organization / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / cell migration / signaling receptor complex adaptor activity / scaffold protein binding / postsynaptic density / negative regulation of cell population proliferation / lipid binding / protein-containing complex binding / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / Nck2, SH3 domain 1 / Nck2, SH3 domain 2 ...Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / : / Variant SH3 domain / 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
ISOPROPYL ALCOHOL / Translocated intimin receptor Tir / Cytoplasmic protein NCK2 / Translocated intimin receptor Tir
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.2May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOPLASMIC PROTEIN NCK2
L: TRANSLOCATED INTIMIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0944
Polymers12,9152
Non-polymers1782
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.244, 52.188, 58.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOPLASMIC PROTEIN NCK2 / NCK ADAPTOR PROTEIN 2 / SH2/SH3 ADAPTOR PROTEIN NCK-BETA / NCK-2


Mass: 11679.088 Da / Num. of mol.: 1 / Fragment: SH2-DOMAIN, RESIDUES 284-380
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: O43639
#2: Protein/peptide TRANSLOCATED INTIMIN RECEPTOR


Mass: 1236.201 Da / Num. of mol.: 1
Fragment: PHOSPHOPEPTIDE LIGAND OF NCK-SH2, RESIDUES 471-480
Source method: obtained synthetically / Details: THE PEPTIDE WAS SYNTHESIZED CHEMICALLY / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: O50190, UniProt: B7UM99*PLUS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINALLY, RESIDUES GPLGS REMAIN ATTACHED TO NCK2-SH2 FOLLOWING CLEAVAGE OF THE GST-NCK2-SH2 FUSION PROTEIN

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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: 1.98 Å3/Da / Density % sol: 37.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: METHOD: HANGING-DROP, VAPOUR-DIFFUSION PROTEIN CONCENTRATION: 8 MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 50% MPD, 15% ETHANOL, 0.01 M NA2 ACETATE, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2004 / Details: 2 AU COATED X-RAY MIRRORS
RadiationMonochromator: ROEMO TYPE DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 16143 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.1
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.7 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NCK1-TIR

Resolution: 1.45→20.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.162 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 879 5.2 %RANDOM
Rwork0.149 ---
obs0.15 16142 98.5 %-
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: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 10 103 984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211031
X-RAY DIFFRACTIONr_bond_other_d0.0040.02706
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9651410
X-RAY DIFFRACTIONr_angle_other_deg1.90731734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7255135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84124.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60115189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.188157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021184
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02218
X-RAY DIFFRACTIONr_nbd_refined0.2170.2157
X-RAY DIFFRACTIONr_nbd_other0.2140.2732
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2484
X-RAY DIFFRACTIONr_nbtor_other0.130.2581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2852625
X-RAY DIFFRACTIONr_mcbond_other0.5822239
X-RAY DIFFRACTIONr_mcangle_it3.1183989
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7852465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9583413
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: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 67 -
Rwork0.176 1069 -
obs--95.62 %
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)
12.078-0.1175-0.63390.91740.5821.6084-0.0418-0.026-0.01260.05540.01120.02630.0554-0.01660.0306-0.0530.0041-0.0023-0.05550.0133-0.02599.81151.218.659
23.80512.5145-0.527410.18912.64327.03170.0061-0.3238-0.36740.8870.059-0.86240.4510.4425-0.0651-0.04780.0694-0.0449-0.02460.07150.010315.70247.56426.206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A283 - 380
2X-RAY DIFFRACTION2L471 - 479

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