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- PDB-2mfq: NMR solution structures of FRS2a PTB domain with neurotrophin rec... -

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Basic information

Entry
Database: PDB / ID: 2mfq
TitleNMR solution structures of FRS2a PTB domain with neurotrophin receptor TrkB
Components
  • BDNF/NT-3 growth factors receptor
  • Fibroblast growth factor receptor substrate 2
KeywordsTRANSFERASE
Function / homology
Function and homology information


lens placode formation involved in camera-type eye formation / brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development ...lens placode formation involved in camera-type eye formation / brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development / cell surface receptor protein tyrosine phosphatase signaling pathway / brain-derived neurotrophic factor binding / negative regulation of cardiac muscle cell differentiation / lens fiber cell development / trans-synaptic signaling by BDNF, modulating synaptic transmission / mechanoreceptor differentiation / anterior/posterior axis specification, embryo / neurotrophin binding / Activated NTRK2 signals through CDK5 / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / phosphatase activator activity / fibroblast growth factor receptor binding / NGF-independant TRKA activation / myelination in peripheral nervous system / organ induction / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of epithelial cell proliferation / gastrulation with mouth forming second / glutamate secretion / feeding behavior / positive regulation of synapse assembly / neuronal action potential propagation / RND1 GTPase cycle / RND2 GTPase cycle / ventricular septum development / positive regulation of axonogenesis / Signaling by ALK / regulation of GTPase activity / Frs2-mediated activation / PI-3K cascade:FGFR3 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / central nervous system neuron development / negative regulation of amyloid-beta formation / oligodendrocyte differentiation / negative regulation of anoikis / RET signaling / Activated NTRK2 signals through RAS / PI3K Cascade / neuroblast proliferation / fibroblast growth factor receptor signaling pathway / vasculogenesis / Activated NTRK2 signals through FRS2 and FRS3 / endomembrane system / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / axon terminus / forebrain development / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / cellular response to brain-derived neurotrophic factor stimulus / Signaling by FGFR1 in disease / regulation of ERK1 and ERK2 cascade / learning / long-term synaptic potentiation / adherens junction / Negative regulation of FGFR3 signaling / cellular response to amino acid stimulus / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / neuron migration / receptor protein-tyrosine kinase / terminal bouton / neuron differentiation / cerebral cortex development / positive regulation of neuron projection development / circadian rhythm / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / Signaling by ALK fusions and activated point mutants / PIP3 activates AKT signaling / positive regulation of peptidyl-serine phosphorylation / early endosome membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protease binding / regulation of apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / positive regulation of MAPK cascade
Similarity search - Function
FRS2, PTB domain / BDNF/NT-3 growth factors receptor NTRK2 / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Phosphotyrosine-binding domain / IRS-type PTB domain ...FRS2, PTB domain / BDNF/NT-3 growth factors receptor NTRK2 / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Leucine rich repeat / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
BDNF/NT-3 growth factors receptor / Fibroblast growth factor receptor substrate 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZeng, L. / Zhou, M.
CitationJournal: Proteins / Year: 2014
Title: Structural insights into FRS2 alpha PTB domain recognition by neurotrophin receptor TrkB.
Authors: Zeng, L. / Kuti, M. / Mujtaba, S. / Zhou, M.M.
History
DepositionOct 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor receptor substrate 2
B: BDNF/NT-3 growth factors receptor


Theoretical massNumber of molelcules
Total (without water)15,9952
Polymers15,9952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2076.7 Å2
ΔGint-19.1 kcal/mol
Surface area7963.3 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fibroblast growth factor receptor substrate 2 / FGFR substrate 2 / FGFR-signaling adaptor SNT / Suc1-associated neurotrophic factor target 1 / SNT-1


Mass: 13441.048 Da / Num. of mol.: 1 / Fragment: IRS-type PTB domain, residues 11-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WU20
#2: Protein/peptide BDNF/NT-3 growth factors receptor / GP145-TrkB / Trk-B / Neurotrophic tyrosine kinase receptor type 2 / TrkB tyrosine kinase / ...GP145-TrkB / Trk-B / Neurotrophic tyrosine kinase receptor type 2 / TrkB tyrosine kinase / Tropomyosin-related kinase B


Mass: 2553.882 Da / Num. of mol.: 1 / Fragment: UNP residues 497-519 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q16620, receptor protein-tyrosine kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1223D HNz(CO)CACB
1323D 1H-15N NOESY
1423D 1H-15N TOCSY
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D 13C-edited 13C/15N-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 0.5 mM [U-100% 2H] EDTA, 100% D2O100% D2O
2100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 0.5 mM [U-100% 2H] EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium phosphate-11
5 mMDTT-2[U-100% 2H]1
0.5 mMEDTA-3[U-100% 2H]1
100 mMsodium phosphate-42
5 mMDTT-5[U-100% 2H]2
0.5 mMEDTA-6[U-100% 2H]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.04Johnson, One Moon Scientificpeak picking
NMRView5.04Johnson, One Moon Scientificdata analysis
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2544 / NOE intraresidue total count: 1006 / NOE long range total count: 871 / NOE medium range total count: 283 / NOE sequential total count: 384 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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