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- PDB-3mxy: Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a... -

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Basic information

Entry
Database: PDB / ID: 3mxy
TitleStructures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications.
Components
  • AICD peptide E683V variant
  • Growth factor receptor-bound protein 2GRB2
KeywordsPROTEIN BINDING / Protein-peptide complex / AICD / Grb2-SH2 / ALZHEIMER'S DISEASE / APP
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / Signaling by cytosolic FGFR1 fusion mutants / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / Interleukin-15 signaling / axon midline choice point recognition / astrocyte activation involved in immune response / MET activates PTPN11 / regulation of spontaneous synaptic transmission / MET activates RAP1 and RAC1 / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / ciliary rootlet / Signal regulatory protein family interactions / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Regulation of KIT signaling / epidermal growth factor receptor binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / STAT5 activation downstream of FLT3 ITD mutants / dendrite development / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / regulation of MAPK cascade / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / neuromuscular process controlling balance / RHOU GTPase cycle / regulation of presynapse assembly / The NLRP3 inflammasome / PI3K events in ERBB2 signaling / intracellular copper ion homeostasis / transition metal ion binding / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / regulation of multicellular organism growth / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / negative regulation of neuron differentiation / insulin receptor substrate binding / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / ECM proteoglycans / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / spindle midzone / positive regulation of T cell migration / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / amyloid A4 / Amyloidogenic glycoprotein / SH2 domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / SHC Adaptor Protein / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / 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 / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSen, U. / Das, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Functional Implications of the Conformational Switch in AICD Peptide upon Binding to Grb2-SH2 Domain.
Authors: Das, S. / Raychaudhuri, M. / Sen, U. / Mukhopadhyay, D.
History
DepositionMay 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Nov 2, 2011Group: Database references
Revision 1.4Dec 14, 2011Group: Database references
Revision 1.5Sep 6, 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 / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 2
L: AICD peptide E683V variant


Theoretical massNumber of molelcules
Total (without water)12,8642
Polymers12,8642
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-8 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.980, 58.980, 117.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-258-

HOH

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Components

#1: Protein Growth factor receptor-bound protein 2 / GRB2 / Adapter protein GRB2 / SH2/SH3 adapter GRB2 / Protein Ash


Mass: 11729.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Plasmid: pET(28a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62993
#2: Protein/peptide AICD peptide E683V variant


Mass: 1135.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P05067*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris ,0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2009 / Details: Osmic Max-flux
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 5748 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.0459 / Net I/σ(I): 5.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.141

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.2refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JYR

1jyr


Resolution: 2.3→29.49 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1212716.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 295 5.1 %RANDOM
Rwork0.232 ---
obs0.232 5748 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7798 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å20 Å20 Å2
2--4.77 Å20 Å2
3----9.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 0 122 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.071 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.406 33 4.7 %
Rwork0.33 662 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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