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- PDB-3buk: Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex -

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Basic information

Entry
Database: PDB / ID: 3buk
TitleCrystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex
Components
  • Neurotrophin-3
  • Tumor necrosis factor receptor superfamily member 16
KeywordsSIGNALING PROTEIN / Ligand-receptor complex / BETA-sheet / Neurotrophin-3 / p75NTR / Cleavage on pair of basic residues / Glycoprotein / Growth factor / Secreted / Apoptosis / Developmental protein / Differentiation / Membrane / Neurogenesis / Transmembrane
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NTF3 activates NTRK3 signaling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NTF3 activates NTRK3 signaling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes / Signaling by NTRK3 (TRKC) / death receptor activity / nerve growth factor receptor binding / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / positive regulation of synaptic transmission, cholinergic / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of dendritic spine development / neurotrophin binding / positive regulation of myelination / nerve growth factor signaling pathway / nerve development / clathrin-coated endocytic vesicle / nerve growth factor binding / induction of positive chemotaxis / peripheral nervous system development / neurotrophin TRKA receptor binding / positive regulation of neural precursor cell proliferation / Activated NTRK3 signals through PI3K / activation of GTPase activity / regulation of reactive oxygen species metabolic process / negative regulation of mitochondrial depolarization / regulation of neuron differentiation / skin development / hair follicle morphogenesis / positive regulation of Rho protein signal transduction / neuronal cell body membrane / chemoattractant activity / skeletal muscle cell differentiation / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / positive regulation of excitatory postsynaptic potential / positive regulation of receptor internalization / Rho protein signal transduction / Activated NTRK3 signals through RAS / hair follicle development / fibroblast growth factor receptor signaling pathway / coreceptor activity / dendrite membrane / cell surface receptor protein tyrosine kinase signaling pathway / presynaptic modulation of chemical synaptic transmission / positive regulation of neuron differentiation / activation of protein kinase B activity / negative regulation of angiogenesis / negative regulation of cell migration / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / central nervous system development / positive regulation of apoptotic signaling pathway / axon guidance / intracellular protein transport / growth factor activity / positive regulation of MAP kinase activity / circadian regulation of gene expression / modulation of chemical synaptic transmission / neuromuscular junction / memory / small GTPase binding / positive regulation of neuron projection development / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / circadian rhythm / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / cell-cell junction / synaptic vesicle / presynapse / positive regulation of peptidyl-serine phosphorylation / cell-cell signaling / negative regulation of neuron projection development / glucose homeostasis / nuclear envelope / presynaptic membrane / nervous system development / amyloid-beta binding / cellular response to oxidative stress / growth cone / fibroblast proliferation / regulation of gene expression / perikaryon / regulation of apoptotic process / neuron apoptotic process / negative regulation of neuron apoptotic process
Similarity search - Function
Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site ...Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / Nerve growth factor family profile. / 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 (NGF or beta-NGF) / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Cystine-knot cytokine / Death-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 16 / Neurotrophin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, T. / Gong, Y. / Cao, P. / Yu, H.J.
CitationJournal: Nature / Year: 2008
Title: Crystal structure of the neurotrophin-3 and p75NTR symmetrical complex.
Authors: Gong, Y. / Cao, P. / Yu, H.J. / Jiang, T.
History
DepositionJan 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotrophin-3
B: Neurotrophin-3
C: Tumor necrosis factor receptor superfamily member 16
D: Tumor necrosis factor receptor superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8616
Polymers63,4194
Non-polymers4422
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-32 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.8, 125.8, 133.1
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Neurotrophin-3 / NT-3 / Neurotrophic factor / HDNF / Nerve growth factor 2 / NGF-2


Mass: 13649.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20783
#2: Protein Tumor necrosis factor receptor superfamily member 16 / Low-affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / Low affinity neurotrophin ...Low-affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR


Mass: 18059.869 Da / Num. of mol.: 2 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ngfr, Tnfrsf16 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07174
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5
Details: 0.9M Lithium Sulfate, 0.05M Na Citrate, 0.7M Ammonium Sulfate, pH 5.0, EVAPORATION, temperature 290K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.003 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 23326 / % possible obs: 96.2 % / Redundancy: 4 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.381 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NT3

1nt3


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.552 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28771 1190 5.1 %RANDOM
Rwork0.22422 ---
all0.22749 22069 --
obs0.22749 22069 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 28 143 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9515754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9525536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.96425.104192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.34815666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8141524
X-RAY DIFFRACTIONr_chiral_restr0.1280.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023222
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.21736
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22844
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4731.52686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.61724334
X-RAY DIFFRACTIONr_scbond_it2.05331532
X-RAY DIFFRACTIONr_scangle_it2.9424.51420
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 97 -
Rwork0.293 1682 -
obs--97.8 %

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