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- PDB-1mil: TRANSFORMING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1mil
TitleTRANSFORMING PROTEIN
ComponentsSHC ADAPTOR PROTEIN
KeywordsTRANSFORMING PROTEIN / SH2 DOMAIN / PHOSPHORYLATION / COLLAGEN / GROWTH REGULATION / ALTERNATIVE INITIATION
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 / Shc-EGFR complex / Signaling by LTK / epidermal growth factor binding ...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 / Shc-EGFR complex / Signaling by LTK / epidermal growth factor binding / epidermal growth factor receptor binding / Signaling by ALK / RET signaling / Activated NTRK3 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signal attenuation / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SHC-mediated cascade:FGFR1 / Tie2 Signaling / insulin-like growth factor receptor binding / SHC1 events in EGFR signaling / phosphotyrosine residue binding / ephrin receptor binding / Integrin signaling / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / FCERI mediated Ca+2 mobilization / negative regulation of angiogenesis / insulin-like growth factor receptor signaling pathway / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / insulin receptor binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / cellular response to growth factor stimulus / phospholipid binding / receptor tyrosine kinase binding / cell-cell adhesion / Signaling by CSF1 (M-CSF) in myeloid cells / GPER1 signaling / Signaling by ALK fusions and activated point mutants / DAP12 signaling / insulin receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / heart development / actin cytoskeleton organization / RAF/MAP kinase cascade / angiogenesis / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 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 / SHC Adaptor Protein / SH2 domain ...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 / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsMikol, V.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of the SH2 domain from the adaptor protein SHC: a model for peptide binding based on X-ray and NMR data.
Authors: Mikol, V. / Baumann, G. / Zurini, M.G. / Hommel, U.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization of the Complex between Cyclophilin a and Cyclosporin Derivatives: The Use of Cross-Seeding
Authors: Mikol, V. / Duc, D.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: X-Ray Structure of a Monomeric Cyclophilin A-Cyclosporin a Crystal Complex at 2.1 A Resolution
Authors: Mikol, V. / Kallen, J. / Pflugl, G. / Walkinshaw, M.D.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: A Novel Transforming Protein (Shc) with an Sh2 Domain is Implicated in Mitogenic Signal Transduction
Authors: Pelicci, G. / Lanfrancone, L. / Grignani, F. / Mcglade, J. / Cavallo, F. / Forni, G. / Nicoletti, I. / Grignani, F. / Pawson, T. / Pelicci, P.G.
History
DepositionSep 20, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHC ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,7131
Polymers11,7131
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.370, 41.550, 97.540
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 SHC ADAPTOR PROTEIN


Mass: 11713.277 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE RECOGNITION DOMAIN SH2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: T7 / Plasmid: T7 / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P29353
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE ARG 16 OF SHC ADOPTS ALTERNATE CONFORMATIONS.
Sequence detailsRESIDUES 1 AND 2 CORRESPOND TO RESIDUES OF THE T7 GENE LEADER SEQUENCE REQUIRED FOR EXPRESSION AND ...RESIDUES 1 AND 2 CORRESPOND TO RESIDUES OF THE T7 GENE LEADER SEQUENCE REQUIRED FOR EXPRESSION AND RESIDUES 3 - 104 CORRESPOND TO RESIDUES 372 - 473 IN THE FULL LENGTH PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal
*PLUS
Density % sol: 46.2 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1dropNa2HPO4/citrate
29 %(w/v)PEG80001drop
31 mMdithiothreitol1drop
40.02 %(w/v)1dropNaN3
51 mMShc1drop
6100 mM1reservoirNa2HPO4/citrate
718 %(w/v)PEG80001reservoir
80.04 %(w/v)1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 3028 / % possible obs: 94 % / Observed criterion σ(I): 2
Reflection
*PLUS
Num. measured all: 7344 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.173 -
obs0.173 2943
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 0 85 881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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