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- PDB-8oyd: TrkB transmembrane domain NMR structure in DMPC/DHPC bicelles -

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Basic information

Entry
Database: PDB / ID: 8oyd
TitleTrkB transmembrane domain NMR structure in DMPC/DHPC bicelles
ComponentsBDNF/NT-3 growth factors receptor
KeywordsTRANSFERASE / PROTEIN / RECEPTOR / NEUROTROPHIN / BDNF / NT-4 / TMD / DIMER
Function / homology
Function and homology information


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 / trans-synaptic signaling by BDNF, modulating synaptic transmission / peripheral nervous system neuron development / brain-derived neurotrophic factor binding ...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 / trans-synaptic signaling by BDNF, modulating synaptic transmission / peripheral nervous system neuron development / brain-derived neurotrophic factor binding / mechanoreceptor differentiation / neurotrophin binding / Activated NTRK2 signals through CDK5 / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / NGF-independant TRKA activation / myelination in peripheral nervous system / Activated NTRK2 signals through PI3K / positive regulation of axonogenesis / feeding behavior / positive regulation of synapse assembly / neuronal action potential propagation / glutamate secretion / regulation of GTPase activity / negative regulation of amyloid-beta formation / central nervous system neuron development / oligodendrocyte differentiation / negative regulation of anoikis / Activated NTRK2 signals through RAS / Activated NTRK2 signals through FRS2 and FRS3 / vasculogenesis / cellular response to brain-derived neurotrophic factor stimulus / axon terminus / learning / cellular response to amino acid stimulus / long-term synaptic potentiation / neuron migration / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / terminal bouton / cerebral cortex development / neuron differentiation / positive regulation of neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / circadian rhythm / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / early endosome membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / protein autophosphorylation / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / negative regulation of neuron apoptotic process / dendritic spine / positive regulation of MAPK cascade / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / receptor complex / postsynaptic density / axon / positive regulation of cell population proliferation / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
BDNF/NT-3 growth factors receptor NTRK2 / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / 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 ...BDNF/NT-3 growth factors receptor NTRK2 / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / 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. / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine rich repeat / : / 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 / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Similarity search - Domain/homology
BDNF/NT-3 growth factors receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKot, E.F. / Mineev, K.S. / Goncharuk, S.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation22-14-00130 Russian Federation
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for the transmembrane signaling and antidepressant-induced activation of the receptor tyrosine kinase TrkB.
Authors: Kot, E.F. / Goncharuk, S.A. / Franco, M.L. / McKenzie, D.M. / Arseniev, A.S. / Benito-Martinez, A. / Costa, M. / Cattaneo, A. / Hristova, K. / Vilar, M. / Mineev, K.S.
History
DepositionMay 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BDNF/NT-3 growth factors receptor
B: BDNF/NT-3 growth factors receptor


Theoretical massNumber of molelcules
Total (without water)9,9502
Polymers9,9502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, In an additional experiment we added the isotopically unlabeled TMD and observed the intermolecular contacts in the 13C-filtered 3D NOESY
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1190 Å2
ΔGint-17 kcal/mol
Surface area8480 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: 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: 4975.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In the constraint files, the local numeration starts from M1 for chain A and from M101 for chain B.
Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK2, TRKB / Variant: TK+ / Plasmid: pGEMEX-1
Cell (production host): Cell-free expression system, lysate-based
Production host: Escherichia coli (E. coli)
References: UniProt: Q16620, receptor protein-tyrosine kinase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aliphatic
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-15N TROSY HSQC
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D HNCO
171isotropic13D HN(CO)CA
181isotropic13D HN(CA)CO
191isotropic13D 1H-13C NOESY aliphatic
1101isotropic12D (H)CCH-TOCSY
1111isotropic13D 1H-13C-NOESY, 13C-filtered
1121isotropic21D 1H
1131isotropic22D 1H-15N HSQC

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Sample preparation

DetailsType: bicelle
Contents: 5 % v/v [U-2H] D2O, 1.1 mM [U-100% 13C; U-100% 15N] High affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB), 9.6 mM [U-2H] DMPC, 42.7 mM [U-2H] DHPC, 1.0 mM n. ...Contents: 5 % v/v [U-2H] D2O, 1.1 mM [U-100% 13C; U-100% 15N] High affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB), 9.6 mM [U-2H] DMPC, 42.7 mM [U-2H] DHPC, 1.0 mM n.a. TCEP, 0.01 % w/v n.a. sodium azide, 20.0 mM n.a. sodium phosphate buffer, 0.5 mM d4 TSP, 95% H2O/5% D2O
Label: 13C-15N-labeled TrkBtm / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 % v/vD2O[U-2H]1
1.1 mMHigh affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB)[U-100% 13C; U-100% 15N]1
9.6 mMDMPC[U-2H]1
42.7 mMDHPC[U-2H]1
1.0 mMTCEPn.a.1
0.01 % w/vsodium aziden.a.1
20.0 mMsodium phosphate buffern.a.1
0.5 mMTSPd41
Sample conditionsIonic strength: 20 mM / Ionic strength err: 0.1 / Label: bicelles / pH: 6 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 313 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001cryogenic triple resonance probe
Bruker AVANCEBrukerAVANCE7002room temperature triple resonance probe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.5Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3.2Bruker Biospincollection
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
TopSpin3.2Bruker Biospinprocessing
TALOS-NShen and Baxstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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