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- PDB-1b8k: Neurotrophin-3 from Human -

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Basic information

Entry
Database: PDB / ID: 1b8k
TitleNeurotrophin-3 from Human
ComponentsPROTEIN (NEUROTROPHIN-3)
KeywordsHORMONE/GROWTH FACTOR / COMPLEX (GROWTH FACTOR-GROWTH FACTOR) / NEUROTROPHIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


NTF3 activates NTRK3 signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / nerve growth factor signaling pathway / nerve development / induction of positive chemotaxis / Activated NTRK3 signals through PI3K / chemoattractant activity ...NTF3 activates NTRK3 signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / nerve growth factor signaling pathway / nerve development / induction of positive chemotaxis / Activated NTRK3 signals through PI3K / chemoattractant activity / positive regulation of receptor internalization / Activated NTRK3 signals through RAS / neuron projection morphogenesis / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / modulation of chemical synaptic transmission / Constitutive Signaling by Aberrant PI3K in Cancer / synaptic vesicle / cell-cell signaling / nervous system development / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / signaling receptor binding / axon / positive regulation of cell population proliferation / dendrite / signal transduction / extracellular space / extracellular region
Similarity search - Function
Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / 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) ...Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / 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) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRobinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y. / Choe, S.
Citation
Journal: Protein Sci. / Year: 1999
Title: The structures of the 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.
#1: Journal: Biochemistry / Year: 1993
Title: Heterodimers of the Neurotrophic Factors: Formation, Isolation, and Differential Stability
Authors: Radziejewski, C. / Robinson, R.C.
History
DepositionFeb 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
A: PROTEIN (NEUROTROPHIN-3)


Theoretical massNumber of molelcules
Total (without water)13,6491
Polymers13,6491
Non-polymers00
Water43224
1
A: PROTEIN (NEUROTROPHIN-3)

A: PROTEIN (NEUROTROPHIN-3)


Theoretical massNumber of molelcules
Total (without water)27,2992
Polymers27,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)38.300, 52.300, 67.700
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 PROTEIN (NEUROTROPHIN-3) / NT3


Mass: 13649.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SUPPLIED BY REGENERON PHARM. / Production host: Escherichia coli (E. coli) / References: UniProt: P20783
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.6
Details: CRYSTALLIZATION CONDITIONS: 7% ISOPROPANOL 185 MM NACITRATE PH 5.6
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris-HCl1drop
322 %PEG80001reservoir
4100 mMPIPES1reservoir
524 amino acid peptide1drop1:2 ratio (NT4 protomer:peptide)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.94
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 7414 / % possible obs: 82 % / Redundancy: 2 % / Rmerge(I) obs: 0.047

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNF

1bnf


Resolution: 2.15→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.302 -5 %RANDOM
Rwork0.238 ---
obs0.238 7414 82 %-
Displacement parametersBiso mean: 42.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 0 24 750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.15
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.3 Å2

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