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- PDB-4xwx: Crystal structure of the PTB domain of SHC -

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Basic information

Entry
Database: PDB / ID: 4xwx
TitleCrystal structure of the PTB domain of SHC
ComponentsSHC-transforming protein 1
KeywordsSIGNALING PROTEIN / phosphotyrosine binding domain / signal transduction / Structural Genomics Consortium (SGC)
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 / Shc-EGFR complex / Interleukin-2 signaling / epidermal growth factor binding / epidermal growth factor receptor 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 / Shc-EGFR complex / Interleukin-2 signaling / epidermal growth factor binding / epidermal growth factor receptor binding / Signaling by ALK / Signaling by ALK fusions and activated point mutants / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / Tie2 Signaling / SHC1 events in EGFR signaling / insulin-like growth factor receptor binding / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Integrin signaling / negative regulation of angiogenesis / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / phospholipid binding / Constitutive Signaling by EGFRvIII / insulin receptor binding / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / cell-cell adhesion / receptor tyrosine kinase binding / cellular response to growth factor stimulus / GPER1 signaling / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / heart development / actin cytoskeleton organization / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / mitochondrial matrix / intracellular signal transduction / defense response to bacterium / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / SH2 domain / Src homology 2 (SH2) domain profile. ...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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsChaikuad, A. / Tallant, C. / Krojer, T. / Dixon-Clarke, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of the PTB domain of SHC
Authors: Chaikuad, A. / Tallant, C. / Krojer, T. / Dixon-Clarke, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHC-transforming protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5298
Polymers18,1341
Non-polymers3957
Water1,820101
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint8 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.910, 126.790, 50.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#1: Protein 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: 18133.912 Da / Num. of mol.: 1 / Fragment: residues 37-201
Source method: isolated from a genetically manipulated source
Details: residues 37-201 / Source: (gene. exp.) Homo sapiens (human) / Gene: SHC1, SHC, SHCA / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P29353
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M sodium/potassium tartrate, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.87→28.98 Å / Num. all: 17585 / Num. obs: 17581 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementResolution: 1.87→28.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 7.053 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19096 912 5.2 %RANDOM
Rwork0.16764 ---
obs0.16887 16660 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.944 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-0 Å2
2--0.75 Å20 Å2
3----2.47 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: 1 / Resolution: 1.87→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 25 101 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191253
X-RAY DIFFRACTIONr_bond_other_d0.0020.021221
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9741686
X-RAY DIFFRACTIONr_angle_other_deg0.91332807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45323.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29215210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.51159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5312.608642
X-RAY DIFFRACTIONr_mcbond_other1.5192.606641
X-RAY DIFFRACTIONr_mcangle_it2.3453.902800
X-RAY DIFFRACTIONr_mcangle_other2.3453.903801
X-RAY DIFFRACTIONr_scbond_it2.163.018611
X-RAY DIFFRACTIONr_scbond_other2.1563.018611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2954.327885
X-RAY DIFFRACTIONr_long_range_B_refined8.05122.2771392
X-RAY DIFFRACTIONr_long_range_B_other8.04922.3031393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 68 -
Rwork0.304 1192 -
obs--99.76 %
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)
12.3711-0.91990.35543.3709-1.06122.8293-0.2193-0.1410.5161-0.04050.1614-0.05730.4664-0.05030.05790.15880.0044-0.03010.0147-0.02950.12893.66115.7951.134
24.5884-0.53212.46924.0164-1.426411.20020.1062-0.30040.54530.20340.0387-0.3208-0.2376-0.0008-0.14490.1209-0.0756-0.03190.0779-0.07760.393612.11631.0626.339
32.80460.02530.57324.1507-0.82364.3639-0.06680.10270.48130.1021-0.0451-0.54650.25690.22670.11180.0764-0.00860.00060.02080.0070.17848.01718.534-0.791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 65
2X-RAY DIFFRACTION2A66 - 112
3X-RAY DIFFRACTION3A113 - 201

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