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- PDB-1wwb: LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1wwb
TitleLIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR
ComponentsPROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB)
KeywordsTRANSFERASE / TRK RECEPTOR / RECEPTOR TYROSINE KINASE / 3D-DOMAIN SWAPPING
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 / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BDNF/NT-3 growth factors receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWiesmann, C. / Ultsch, M.H. / Bass, S.H. / De Vos, A.M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of the neurotrophin-binding domain of TrkA, TrkB and TrkC.
Authors: Ultsch, M.H. / Wiesmann, C. / Simmons, L.C. / Henrich, J. / Yang, M. / Reilly, D. / Bass, S.H. / de Vos, A.M.
History
DepositionMay 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: PROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB)


Theoretical massNumber of molelcules
Total (without water)11,8021
Polymers11,8021
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.340, 68.340, 124.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein PROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB)


Mass: 11802.254 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q16620
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.55 Å3/Da / Density % sol: 65.34 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.3 mg/mlprotein1drop
2100 mM1dropNaCl
317 mMbicine1drop
40.83 mMAEBSF1drop
55.8 %satammonium sulfate1drop
60.17 %(v/v)MPD1drop
745 %satammonium sulfate1reservoir
81 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorDate: Mar 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 115960 / % possible obs: 98.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.019 / % possible all: 97.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WWC

1wwc


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2
Details: THE MOLECULE UNDERGOES 3D-DOMAIN SWAPPING, SUCH THAT STRAND A OF ONE MOLECULE REPLACES THE SAME STRAND A OF A SYMMETRY RELATED MATE
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1018 9.5 %RANDOM
Rwork0.247 ---
obs-10367 97.77 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 0 74 906
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.8352
X-RAY DIFFRACTIONx_mcangle_it4.7093
X-RAY DIFFRACTIONx_scbond_it4.7994.5
X-RAY DIFFRACTIONx_scangle_it7.4825.5
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 0.2 / % reflection Rfree: 9.5 % / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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