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- PDB-1hcf: Crystal structure of TrkB-d5 bound to neurotrophin-4/5 -

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Basic information

Entry
Database: PDB / ID: 1hcf
TitleCrystal structure of TrkB-d5 bound to neurotrophin-4/5
Components
  • BDNF/NT-3 GROWTH FACTORS RECEPTOR
  • NEUROTROPHIN-4
KeywordsTRANSFERASE/HORMONE / COMPLEX(TRANSFERASE-GROWTH FACTOR) / NEUROTROPHIN-4/5 / TRKB RECEPTOR / NGF-BETA SUPERFAMILY / IMMUNOGLOBULIN DOMAIN / TRANSFERASE-HORMONE complex
Function / homology
Function and homology information


taste bud development / sensory organ boundary specification / ganglion mother cell fate determination / 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 ...taste bud development / sensory organ boundary specification / ganglion mother cell fate determination / 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 / nerve growth factor receptor binding / ameloblast differentiation / trans-synaptic signaling by BDNF, modulating synaptic transmission / mechanoreceptor differentiation / neurotrophin binding / Activated NTRK2 signals through CDK5 / nerve growth factor signaling pathway / NTRK2 activates RAC1 / nerve development / 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 / innervation / 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 / epidermis development / long-term memory / Activated NTRK2 signals through FRS2 and FRS3 / vasculogenesis / neuron projection morphogenesis / cellular response to brain-derived neurotrophic factor stimulus / axon terminus / cell surface receptor protein tyrosine kinase signaling pathway / adult locomotory behavior / learning / cellular response to amino acid stimulus / growth factor activity / positive regulation of neuron projection development / circadian rhythm / receptor protein-tyrosine kinase / cerebral cortex development / modulation of chemical synaptic transmission / long-term synaptic potentiation / neuron migration / neuron differentiation / terminal bouton / Constitutive Signaling by Aberrant PI3K in Cancer / synaptic vesicle / 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 / extracellular space / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Neurotrophin-4 / BDNF/NT-3 growth factors receptor NTRK2 / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / Growth factor receptor NTRK ...Neurotrophin-4 / BDNF/NT-3 growth factors receptor NTRK2 / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Cystine-knot cytokine / 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 / Ribbon / 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
Neurotrophin-4 / BDNF/NT-3 growth factors receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBanfield, M.J. / Naylor, R.L. / Robertson, A.G.S. / Allen, S.J. / Dawbarn, D. / Brady, R.L.
Citation
Journal: Structure / Year: 2001
Title: Specificity in Trk-Receptor:Neurotrophin Interaction: The Crystal Structure of Trkb-D5 in Complex with Neurotrophin-4/5
Authors: Banfield, M.J. / Naylor, R.L. / Robertson, A.G.S. / Allen, S.J. / Dawbarn, D. / Brady, R.L.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2001
Title: Identification and Structure of the Nerve Growth Factor Binding Site on Trka
Authors: Robertson, A.G.S. / Banfield, M.J. / Allen, S.J. / Dando, J.A. / Mason, G.G.F. / Tyler, S.J. / Bennett, G.S. / Brain, S.D. / Clarke, A.R. / Brady, R.L. / Dawbarn, D.
#2: Journal: Nature / Year: 1999
Title: Crystal Structure of Nerve Growth Factor in Complex with the Ligand-Binding Domain of the Trka Receptor
Authors: Wiesmann, C. / Ultsch, M.H. / Bass, S.H. / Devos, A.M.
#3: Journal: 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. / Devos, A.M.
#4: Journal: Protein Sci. / Year: 1999
Title: The Structures of Neurotrophin 4 Homodimer and the Brain-Derived Neurotrophic Factor/Neurotrophin 4 Heterodimer Reveal a Common Trk Binding Site
Authors: Robinson, R.C. / Radziejewski, C. / Spraggon, G. / Greenwald, J. / Kostura, M.R. / Burtnick, L.D. / Stuart, D.I. / Choe, S. / Jones, E.Y.
History
DepositionMay 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROTROPHIN-4
B: NEUROTROPHIN-4
X: BDNF/NT-3 GROWTH FACTORS RECEPTOR
Y: BDNF/NT-3 GROWTH FACTORS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3668
Polymers50,9814
Non-polymers3844
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.372, 80.406, 91.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCOMPLEX OF HOMODIMERIC NEUROTROPHIN-4 AND TWO CHAINSOF TRKB

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Components

#1: Protein NEUROTROPHIN-4 / NEUROTROPHIN-5 / NEUROTROPHIN-4/5 / NT-4/5


Mass: 13944.647 Da / Num. of mol.: 2 / Fragment: ACTIVE, FRAGMENT. PRO-REGION CLEAVED / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cellular location: EXTRACELLULAR / References: UniProt: P34130
#2: Protein BDNF/NT-3 GROWTH FACTORS RECEPTOR / TRKB / GP145-TRKB


Mass: 11545.979 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN 5 (RESIDUES 286 - 383)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: PLASMA MEMBRANE / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q16620
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES NUMBERED X283, X284, X285 ARE CLONING ARTEFACTS. THEY ARE DERIVED FROM THE HIS-TAG ...RESIDUES NUMBERED X283, X284, X285 ARE CLONING ARTEFACTS. THEY ARE DERIVED FROM THE HIS-TAG SEQUENCE OF THE PET-15B PLASMID, AND DO NOT CORRESPOND TO THE NATIVE TRKB RESIDUES 283, 284 AND 285. RESIDUES NUMBERED Y283, Y284, Y285 ARE CLONING ARTEFACTS. THEY ARE DERIVED FROM THE HIS-TAG SEQUENCE OF THE PET-15B PLASMID, AND DO NOT CORRESPOND TO THE NATIVE TRKB RESIDUES 283, 284 AND 285.

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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: 2.7 Å3/Da / Density % sol: 46.6 %
Crystal growpH: 7.5
Details: 10 MG/ML COMPLEX IN 20MM TRIS, 150MM NACL, PH 7.5, 100MM HEPES PH 7.5, 1.5M LISO4
Crystal grow
*PLUS
Method: unknown / PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein11
21.5-1.6 M12LiSO4
3100 mMHEPES12pH7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2001 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15635 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 63.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 19.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.294 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.294

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B98 (NEUROTROPHIN), 1WWB (TRK)

1b98

1wwb


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.264 761 4.9 %RANDOM
Rwork0.218 ---
obs0.218 15411 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.14 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---7.91 Å20 Å2
3---7.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 20 60 3499
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5461.5
X-RAY DIFFRACTIONc_mcangle_it1.9972
X-RAY DIFFRACTIONc_scbond_it2.7282
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.359 84 5.5 %
Rwork0.299 1430 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3SO4.PAR
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Rfactor obs: 0.299

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