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- PDB-1b8m: BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4 -

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Basic information

Entry
Database: PDB / ID: 1b8m
TitleBRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4
Components
  • PROTEIN (BRAIN DERIVED NEUROTROPHIC FACTOR)
  • PROTEIN (NEUROTROPHIN-4)
KeywordsGROWTH FACTOR/NEUROTROPHIN-4 / COMPLEX (GROWTH FACTOR-GROWTH FACTOR) / NEUROTROPHIN / GROWTH FACTOR-NEUROTROPHIN-4 COMPLEX
Function / homology
Function and homology information


taste bud development / positive regulation of brain-derived neurotrophic factor receptor signaling pathway / sensory organ boundary specification / ganglion mother cell fate determination / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands ...taste bud development / positive regulation of brain-derived neurotrophic factor receptor signaling pathway / sensory organ boundary specification / ganglion mother cell fate determination / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands / ameloblast differentiation / : / mechanoreceptor differentiation / negative regulation of myotube differentiation / Activated NTRK2 signals through CDK5 / nerve growth factor signaling pathway / NTRK2 activates RAC1 / regulation of protein localization to cell surface / nerve development / collateral sprouting / Activated NTRK2 signals through FYN / positive regulation of collateral sprouting / Activated NTRK2 signals through PI3K / innervation / positive regulation of synapse assembly / negative regulation of apoptotic signaling pathway / Activated NTRK2 signals through RAS / epidermis development / long-term memory / Activated NTRK2 signals through FRS2 and FRS3 / synapse assembly / neuron projection morphogenesis / NPAS4 regulates expression of target genes / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / adult locomotory behavior / growth factor activity / positive regulation of neuron projection development / modulation of chemical synaptic transmission / Constitutive Signaling by Aberrant PI3K in Cancer / synaptic vesicle / nervous system development / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of neuron apoptotic process / endoplasmic reticulum lumen / axon / dendrite / perinuclear region of cytoplasm / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Brain-derived neurotrophic factor / Neurotrophin-4 / 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 ...Brain-derived neurotrophic factor / Neurotrophin-4 / 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
: / : / Neurotrophic factor BDNF precursor form / Neurotrophin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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: 1995
Title: Structure of the Brain-Derived Neurotrophic Factor (Slash)Neurotrophin 3 Heterodimer
Authors: Robinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y.
#2: Journal: Biochemistry / Year: 1993
Title: Heterodimers of the Neurotrophic Factors: Formation, Isolation, and Differential Stability
Authors: Radziejewski, C. / Robinson, R.C.
History
DepositionFeb 1, 1999Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: 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 1.4Nov 20, 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
A: PROTEIN (BRAIN DERIVED NEUROTROPHIC FACTOR)
B: PROTEIN (NEUROTROPHIN-4)


Theoretical massNumber of molelcules
Total (without water)27,4802
Polymers27,4802
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-17 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.700, 105.900, 51.800
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 (BRAIN DERIVED NEUROTROPHIC FACTOR) / BDNF


Mass: 13535.575 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: GenBank: M61176, UniProt: P23560*PLUS
#2: Protein PROTEIN (NEUROTROPHIN-4) / NT4


Mass: 13944.647 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: GenBank: M86528, UniProt: P34130*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.53 Å3/Da / Density % sol: 50 %
Crystal growpH: 6 / Details: pH 6.0
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: 270 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.97
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 7858 / % possible obs: 98 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06

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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: 2.75→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -5 %RANDOM
Rwork0.198 ---
obs-7858 98 %-
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 57 1778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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
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

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