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- PDB-4at3: CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH CPD5N -

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Basic information

Entry
Database: PDB / ID: 4at3
TitleCRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH CPD5N
ComponentsBDNF/NT-3 GROWTH FACTORS RECEPTOR
KeywordsTRANSFERASE
Function / homology
Function and homology information


brain-derived neurotrophic factor binding / brain-derived neurotrophic factor receptor activity / 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 / trans-synaptic signaling by BDNF, modulating synaptic transmission ...brain-derived neurotrophic factor binding / brain-derived neurotrophic factor receptor activity / 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 / trans-synaptic signaling by BDNF, modulating synaptic transmission / mechanoreceptor differentiation / neurotrophin binding / Activated NTRK2 signals through CDK5 / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / NGF-independant TRKA activation / Activated NTRK2 signals through PI3K / myelination in peripheral nervous system / feeding behavior / positive regulation of axonogenesis / neuronal action potential propagation / glutamate secretion / positive regulation of synapse assembly / regulation of GTPase activity / central nervous system neuron development / negative regulation of amyloid-beta formation / 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 / cell surface receptor protein tyrosine kinase signaling pathway / learning / cellular response to amino acid stimulus / positive regulation of neuron projection development / circadian rhythm / receptor protein-tyrosine kinase / cerebral cortex development / long-term synaptic potentiation / neuron migration / neuron differentiation / terminal bouton / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / early endosome membrane / dendritic spine / negative regulation of neuron apoptotic process / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LTI / BDNF/NT-3 growth factors receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Crystal Structures of Trka and Trkb Suggest Key Regions for Achieving Selective Inhibition.
Authors: Bertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M.
History
DepositionMay 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BDNF/NT-3 GROWTH FACTORS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7142
Polymers34,3521
Non-polymers3621
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.331, 94.340, 46.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 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: 34351.695 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 543-838
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q16620, receptor protein-tyrosine kinase
#2: Chemical ChemComp-LTI / (5Z)-5-(carbamoylimino)-3-[(5R)-6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-ylsulfanyl]-2,5-dihydroisothiazole-4-carboxamide


Mass: 362.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.83 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growTemperature: 277 K / pH: 6
Details: THE TRKB-CPD5N COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 1.6 M AMMONIUM SULFATE, 50 MM MES, PH 6.0 AT 4 DEGREESC IN PRESENCE OF 2 MM OF INHIBITOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.77→47.19 Å / Num. obs: 37068 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 23.04 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 94.8

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Processing

Software
NameVersionClassification
BUSTER2.9.7refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ASZ

4asz


Resolution: 1.77→24.87 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9293 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.107
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 3675 9.96 %RANDOM
Rwork0.1974 ---
obs0.2 36906 98.64 %-
Displacement parametersBiso mean: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.5499 Å20 Å20 Å2
2--1.0364 Å20 Å2
3---0.5135 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 1.77→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 24 315 2670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072425HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943277HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d838SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes349HARMONIC5
X-RAY DIFFRACTIONt_it2425HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion16.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion302SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2995SEMIHARMONIC4
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2451 281 10.53 %
Rwork0.2292 2388 -
all0.2309 2669 -
obs--98.64 %

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