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- PDB-4jmh: Crystal structure of synthetic protein in complex with double pY ... -

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Basic information

Entry
Database: PDB / ID: 4jmh
TitleCrystal structure of synthetic protein in complex with double pY peptide
Components
  • Clamp Shc1_pY239/240
  • SHC-transforming protein 1
KeywordsDE NOVO PROTEIN / Synthetic protein / binding to double pY containing sequence
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Interleukin-2 signaling / Signaling by LTK / epidermal growth factor receptor binding / Shc-EGFR complex ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Interleukin-2 signaling / Signaling by LTK / epidermal growth factor receptor binding / Shc-EGFR complex / epidermal growth factor binding / Signaling by ALK / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / Signalling to RAS / Signal attenuation / SHC-related events triggered by IGF1R / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / ephrin receptor binding / Signaling by CSF3 (G-CSF) / Tie2 Signaling / insulin-like growth factor receptor binding / phosphotyrosine residue binding / Integrin signaling / SHC1 events in EGFR signaling / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / negative regulation of angiogenesis / insulin receptor binding / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / cell-cell adhesion / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / phospholipid binding / cellular response to growth factor stimulus / epidermal growth factor receptor signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by ALK fusions and activated point mutants / insulin receptor signaling pathway / DAP12 signaling / GPER1 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / heart development / RAF/MAP kinase cascade / actin cytoskeleton organization / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / intracellular signal transduction / defense response to bacterium / mitochondrial matrix / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / plasma membrane / cytosol
Similarity search - Function
Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
SHC-transforming protein 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.408 Å
AuthorsYasui, N. / Smith, L. / Koide, S.
CitationJournal: Mol.Cell / Year: 2014
Title: Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation.
Authors: Yasui, N. / Findlay, G.M. / Gish, G.D. / Hsiung, M.S. / Huang, J. / Tucholska, M. / Taylor, L. / Smith, L. / Boldridge, W.C. / Koide, A. / Pawson, T. / Koide, S.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Data collection
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clamp Shc1_pY239/240
B: SHC-transforming protein 1


Theoretical massNumber of molelcules
Total (without water)24,0742
Polymers24,0742
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.853, 92.190, 59.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Clamp Shc1_pY239/240


Mass: 22333.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide SHC-transforming protein 1 / SHC-transforming protein 3 / SHC-transforming protein A / Src homology 2 domain-containing- ...SHC-transforming protein 3 / SHC-transforming protein A / Src homology 2 domain-containing-transforming protein C1 / SH2 domain protein C1


Mass: 1739.625 Da / Num. of mol.: 1 / Fragment: unp residues 344-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHC, SHC1, SHCA / Production host: Escherichia coli (E. coli) / References: UniProt: P29353
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.66% ammonium sulfate, 2.32% PEG400, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 9059 / Num. obs: 9059 / % possible obs: 100 % / Observed criterion σ(I): -3 / Net I/σ(I): 21.8

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JMG

4jmg


Resolution: 2.408→32.173 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 438 4.83 %
Rwork0.2128 --
obs0.2158 9059 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.408→32.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 7 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091687
X-RAY DIFFRACTIONf_angle_d1.3722299
X-RAY DIFFRACTIONf_dihedral_angle_d16.281585
X-RAY DIFFRACTIONf_chiral_restr0.097238
X-RAY DIFFRACTIONf_plane_restr0.007293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4077-2.7560.34811460.26722686X-RAY DIFFRACTION87
2.756-3.47160.31771500.24763101X-RAY DIFFRACTION99
3.4716-32.17590.22721420.17852834X-RAY DIFFRACTION88

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