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

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Basic information

Entry
Database: PDB / ID: 3mxc
TitleStructures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications.
Components
  • AICD peptide
  • Growth factor receptor-bound protein 2
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 / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling / amyloid-beta complex / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / microglia development / negative regulation of presynapse assembly / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / MET activates RAP1 and RAC1 / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / astrocyte activation involved in immune response / vesicle membrane / smooth endoplasmic reticulum calcium ion homeostasis / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / NMDA selective glutamate receptor signaling pathway / Signal regulatory protein family interactions / regulation of spontaneous synaptic transmission / epidermal growth factor receptor binding / mating behavior / Regulation of KIT signaling / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / PI-3K cascade:FGFR3 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / natural killer cell mediated cytotoxicity / neuron remodeling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / PI-3K cascade:FGFR1 / suckling behavior / COPII-coated ER to Golgi transport vesicle / positive regulation of actin filament polymerization / endodermal cell differentiation / positive regulation of protein metabolic process / dendrite development / GRB2:SOS provides linkage to MAPK signaling for Integrins / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / presynaptic active zone / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / PI3K events in ERBB2 signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / neuromuscular process controlling balance / transition metal ion binding / SOS-mediated signalling / Activated NTRK3 signals through RAS / regulation of multicellular organism growth / Activated NTRK2 signals through RAS / signal transduction in response to DNA damage / intracellular copper ion homeostasis / fibroblast growth factor receptor signaling pathway / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / regulation of presynapse assembly / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of neuron differentiation / Interleukin receptor SHC signaling / ECM proteoglycans / Signalling to RAS / GAB1 signalosome / spindle midzone / Signal attenuation / positive regulation of T cell migration / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / forebrain development / smooth endoplasmic reticulum / Schwann cell development
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. / 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 precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / SH2 domain / SHC Adaptor Protein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / 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 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 7, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Revision 1.7Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)12,8942
Polymers12,8942
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.369, 59.369, 117.101
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-275-

HOH

21A-315-

HOH

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Components

#1: Protein Growth factor receptor-bound protein 2 / 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


Mass: 1165.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P05067*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K
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
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 2, 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→30 Å / Num. obs: 8497 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 5.48 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.0423 / Rsym value: 0.0343 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.09 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.23 / % possible all: 95

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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→29.69 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1299777.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 442 5.2 %RANDOM
Rwork0.217 ---
obs0.217 8497 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.78 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å20 Å2
2--4.4 Å20 Å2
3----8.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 122 990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it3.052
X-RAY DIFFRACTIONc_scbond_it2.822
X-RAY DIFFRACTIONc_scangle_it4.492.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.329 48 4.8 %
Rwork0.306 952 -
obs--95 %
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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