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- PDB-5mo9: Structure of human TrkB receptor ligand binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 5mo9
TitleStructure of human TrkB receptor ligand binding domain in complex with the Fab frgment of antibody AB20
Components
  • AB20 Fab heavy chain
  • AB20 Fab light chain
  • BDNF/NT-3 growth factors receptor
KeywordsIMMUNE SYSTEM / Trk receptor / antibody / antigen / complex
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 / circadian rhythm / positive regulation of neuron projection development / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsHoerer, S.
CitationJournal: J. Pharmacol. Exp. Ther. / Year: 2017
Title: Pharmaceutical Characterization of Tropomyosin Receptor Kinase B-Agonistic Antibodies on Human Induced Pluripotent Stem (hiPS) Cell-Derived Neurons.
Authors: Traub, S. / Stahl, H. / Rosenbrock, H. / Simon, E. / Florin, L. / Hospach, L. / Horer, S. / Heilker, R.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Jan 17, 2024Group: 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 1.3Nov 13, 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
H: AB20 Fab heavy chain
L: AB20 Fab light chain
X: BDNF/NT-3 growth factors receptor


Theoretical massNumber of molelcules
Total (without water)64,5173
Polymers64,5173
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.370, 55.430, 69.390
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: Antibody AB20 Fab heavy chain


Mass: 23675.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): Epithelium
#2: Antibody AB20 Fab light chain


Mass: 23931.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Epithelium / Organ: Ovary / Cell line (production host): CHO / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): Epithelium
#3: 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: 16909.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment: Ligand binding domain / Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK2, TRKB / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16620, receptor protein-tyrosine kinase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.27 Å3/Da / Density % sol: 44.47 % / Description: rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 6% w/v PEG 3350, 25 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0005 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2014
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0005 Å / Relative weight: 1
ReflectionResolution: 2.594→37.402 Å / Num. obs: 18392 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.158 / Net I/σ(I): 11
Reflection shellResolution: 2.594→2.639 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.744 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSMay 1, 2016 BUILT=20160617data reduction
Aimless0.5.27data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hcf

1hcf


Resolution: 2.594→37 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.466 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.513 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.253
RfactorNum. reflection% reflectionSelection details
Rfree0.224 855 4.65 %RANDOM
Rwork0.19 ---
obs0.182 18392 99.5 %-
Displacement parametersBiso mean: 47.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.7572 Å20 Å20 Å2
2---0.9688 Å20 Å2
3---2.726 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.594→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 0 169 4260
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084299HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1404SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes632HARMONIC5
X-RAY DIFFRACTIONt_it4299HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion18.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion571SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4703SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.385 -3.73 %
Rwork0.221 284 -
all0.229 295 -
obs--6.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13910.2716-0.93610.0131-0.29940.7580.00180.018-0.0203-0.0091-0.00570.00580.01310.00280.00390.0173-0.00820.0097-0.0006-0.0278-0.0048-51.83835.5102-20.7023
20.10950.12270.4220.32820.45060.2681-0.0001-0.0021-0.00080.01330.00390.0146-0.0026-0.0036-0.0038-0.0012-0.00240.00050.0113-0.0090.0112-25.190123.1004-32.2042
30.17430.08170.21931.1006-0.45680.0439-0.0013-0.02340.0056-0.0028-0.0113-0.0132-0.0002-0.01790.01260.00240.0098-0.0019-0.00090.01070.0317-36.827-2.7568-4.7875
40.0894-0.2797-0.38830.15080.28590.0893-0.00180.00240.00150.00050.00010.0019-0.00220.0050.00170.0042-0.00050.0121-0.00230.00340.0031-9.470411.089-27.4351
53.19410.4639-0.90441.3913-1.1431.75420.013-0.01460.0161-0.02320.04780.13660.12390.0293-0.0608-0.1193-0.03160.0243-0.15960.00890.0773-65.4379-21.9292-11.2392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ H|1 H|114 }
2X-RAY DIFFRACTION2{ H|120 H|217 }
3X-RAY DIFFRACTION3{ L|1 L|111 }
4X-RAY DIFFRACTION4{ L|116 L|219 }
5X-RAY DIFFRACTION5{ X|* }

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