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- PDB-2ci9: Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC ... -

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Basic information

Entry
Database: PDB / ID: 2ci9
TitleNck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir
Components
  • CYTOPLASMIC PROTEIN NCK1Cytoplasm
  • TRANSLOCATED INTIMIN RECEPTOR
KeywordsPROTEIN BINDING / PROTEIN-BINDING / SH2-DOMAIN-COMPLEX
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 / DCC mediated attractive signaling / Nephrin family interactions / 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 / molecular condensate scaffold activity / response to endoplasmic reticulum stress / T cell activation / ephrin receptor binding / Downstream signal transduction / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / FCGR3A-mediated phagocytosis / 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 / 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 / nucleus / plasma 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 / Nck1, SH3 domain 1 / Nck1, 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 / 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 / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translocated intimin receptor Tir / Translocated intimin receptor Tir / SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Refinement description / Version format compliance
Revision 1.2May 15, 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_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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 NCK1
B: CYTOPLASMIC PROTEIN NCK1
L: TRANSLOCATED INTIMIN RECEPTOR
M: TRANSLOCATED INTIMIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)26,4394
Polymers26,4394
Non-polymers00
Water4,594255
1
A: CYTOPLASMIC PROTEIN NCK1
L: TRANSLOCATED INTIMIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)13,2202
Polymers13,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7.7 kcal/mol
Surface area6800 Å2
MethodPISA
2
B: CYTOPLASMIC PROTEIN NCK1
M: TRANSLOCATED INTIMIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)13,2202
Polymers13,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-8.3 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.092, 60.518, 65.061
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 NCK1 / Cytoplasm / NCK ADAPTOR PROTEIN 1 / SH2/SH3 ADAPTOR PROTEIN NCK-ALPHA


Mass: 11751.317 Da / Num. of mol.: 2 / 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: Protein/peptide TRANSLOCATED INTIMIN RECEPTOR


Mass: 1468.391 Da / Num. of mol.: 2
Fragment: PHOSPHOPEPTIDE LIGAND OF NCK-SH2, RESIDUES 469-480
Source method: obtained synthetically / Details: THE PEPTIDE WAS SYNTHESIZED CHEMICALLY / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: O50190, UniProt: B7UM99*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: TECHNIQUE: HANGING-DROP, VAPOR-DIFFUSION PROTEIN CONCENTRATION: 8MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 2.4M (NH4)2HPO4, 0.1M TRIS, PH 8.5 CRYOCONDITIONS: 50% MPD

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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: Jun 1, 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: 1.4→30 Å / Num. obs: 38419 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.2 / % possible all: 88

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Processing

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

Resolution: 1.5→28.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.033 / SU ML: 0.059 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1532 5 %RANDOM
Rwork0.196 ---
obs0.198 28813 85.4 %-
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: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 0 255 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212038
X-RAY DIFFRACTIONr_bond_other_d0.0070.021395
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9592775
X-RAY DIFFRACTIONr_angle_other_deg1.57233435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6725261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80924.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25215374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.083158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02411
X-RAY DIFFRACTIONr_nbd_refined0.2030.2322
X-RAY DIFFRACTIONr_nbd_other0.160.21360
X-RAY DIFFRACTIONr_nbtor_refined0.170.2911
X-RAY DIFFRACTIONr_nbtor_other0.0760.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70321244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47331968
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8572892
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5483795
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 119
Rwork0.239 2419
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)
12.28180.56790.11551.5021-0.28781.1550.00220.0367-0.13970.00020.0161-0.05240.08130.0359-0.0184-0.1770.00480.0068-0.0476-0.004-0.146632.6112.6698.711
21.66260.956-0.37991.97730.10223.70320.05310.1040.1057-0.13360.106-0.0448-0.49090.229-0.1591-0.1016-0.01860.0414-0.0261-0.0108-0.130947.04445.189.53
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A275 - 377
2X-RAY DIFFRACTION1L472 - 480
3X-RAY DIFFRACTION2B278 - 377
4X-RAY DIFFRACTION2M470 - 481

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