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- PDB-1a1a: C-SRC (SH2 DOMAIN WITH C188A MUTATION) COMPLEXED WITH ACE-FORMYL ... -

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Basic information

Entry
Database: PDB / ID: 1a1a
TitleC-SRC (SH2 DOMAIN WITH C188A MUTATION) COMPLEXED WITH ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)
Components
  • ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)
  • C-SRC TYROSINE KINASETyrosine-protein kinase CSK
KeywordsCOMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) complex
Function / homology
Function and homology information


regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / positive regulation of hippo signaling ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / positive regulation of hippo signaling / regulation of cell projection assembly / regulation of cell-cell adhesion / positive regulation of dephosphorylation / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / regulation of vascular permeability / entry of bacterium into host cell / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / positive regulation of protein processing / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / connexin binding / focal adhesion assembly / signal complex assembly / response to acidic pH / podosome / negative regulation of telomere maintenance via telomerase / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / DCC mediated attractive signaling / negative regulation of mitochondrial depolarization / adherens junction organization / osteoclast development / myoblast proliferation / EPH-Ephrin signaling / Ephrin signaling / odontogenesis / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / regulation of early endosome to late endosome transport / cellular response to fatty acid / MET activates PTK2 signaling / oogenesis / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / Signaling by ALK / Regulation of KIT signaling / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / Signaling by EGFR / leukocyte migration / phospholipase activator activity / DNA biosynthetic process / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / stress fiber assembly / negative regulation of telomerase activity / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / uterus development / neurotrophin TRK receptor signaling pathway / phospholipase binding / PECAM1 interactions / Long-term potentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / EPH-ephrin mediated repulsion of cells / FCGR activation / negative regulation of anoikis
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily ...SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShewchuk, L. / Jordan, S.
CitationJournal: Biochemistry / Year: 1997
Title: Peptide ligands of pp60(c-src) SH2 domains: a thermodynamic and structural study.
Authors: Charifson, P.S. / Shewchuk, L.M. / Rocque, W. / Hummel, C.W. / Jordan, S.R. / Mohr, C. / Pacofsky, G.J. / Peel, M.R. / Rodriguez, M. / Sternbach, D.D. / Consler, T.G.
History
DepositionDec 10, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Derived calculations
Revision 1.4Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-SRC TYROSINE KINASE
C: ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)
B: C-SRC TYROSINE KINASE
D: ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)


Theoretical massNumber of molelcules
Total (without water)25,7474
Polymers25,7474
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.400, 65.400, 74.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7866, 0.2906, -0.5448), (0.2682, 0.9556, 0.1224), (0.5561, -0.0498, -0.8296)
Vector: 98.5027, -0.3346, 29.4045)

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Components

#1: Protein C-SRC TYROSINE KINASE / Tyrosine-protein kinase CSK


Mass: 12287.820 Da / Num. of mol.: 2 / Fragment: SH2 DOMAIN / Mutation: C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SRC / Plasmid: PET11B / Cellular location (production host): CYTOPLASM / Gene (production host): SRC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12931, EC: 2.7.1.112
#2: Protein/peptide ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)


Mass: 585.626 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / pH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 1.0 M LI2SO4, 2% PEG8000 AT 4C. THE CRYSTAL WAS SOAKED IN 25% GLYCEROL PRIOR TO DATA COLLECTION., pH 8.0, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1125 mg/mlprotein1drop
220 mMHEPES1drop
3350 mM1dropNaCl
45 mMdithiothreitol1drop
55 mMEDTA1drop
61.0 M1reservoirLiSO4
72 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18250 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.68
Reflection shellResolution: 2→2.25 Å / Redundancy: 2.99 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 5.5 / % possible all: 90

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
R-AXISdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHD
Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 2 / Details: PARTIALLY REFINED
RfactorNum. reflection% reflection
Rwork0.198 --
obs0.198 16781 95 %
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 0 194 1934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2→2.1 Å / Total num. of bins used: 8 / % reflection obs: 89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.PTATOPH19.PTA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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