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- PDB-1bnd: STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTRO... -

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Basic information

Entry
Database: PDB / ID: 1bnd
TitleSTRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER
Components
  • BRAIN DERIVED NEUROTROPHIC FACTOR
  • NEUROTROPHIN 3
KeywordsCOMPLEX (GROWTH FACTOR/GROWTH FACTOR) / NEUROTROPHIN / COMPLEX (GROWTH FACTOR-GROWTH FACTOR) COMPLEX
Function / homology
Function and homology information


positive regulation of brain-derived neurotrophic factor receptor signaling pathway / NTF3 activates NTRK3 signaling / BDNF activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands ...positive regulation of brain-derived neurotrophic factor receptor signaling pathway / NTF3 activates NTRK3 signaling / BDNF activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands / : / 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 / induction of positive chemotaxis / Activated NTRK2 signals through PI3K / Activated NTRK3 signals through PI3K / positive regulation of synapse assembly / chemoattractant activity / negative regulation of apoptotic signaling pathway / positive regulation of receptor internalization / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / 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 / growth factor activity / positive regulation of neuron projection development / 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 / endoplasmic reticulum lumen / signaling receptor binding / axon / positive regulation of cell population proliferation / dendrite / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Brain-derived neurotrophic factor / 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. ...Brain-derived neurotrophic factor / 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
ISOPROPYL ALCOHOL / Neurotrophin-3 / Neurotrophic factor BDNF precursor form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRobinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y.
Citation
Journal: Biochemistry / Year: 1995
Title: Structure of the brain-derived neurotrophic factor/neurotrophin 3 heterodimer.
Authors: Robinson, R.C. / Radziejewski, C. / Stuart, D.I. / 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
DepositionDec 12, 1994Processing site: BNL
Revision 1.0Apr 4, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRAIN DERIVED NEUROTROPHIC FACTOR
B: NEUROTROPHIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2513
Polymers27,1912
Non-polymers601
Water1,26170
1
A: BRAIN DERIVED NEUROTROPHIC FACTOR
B: NEUROTROPHIN 3
hetero molecules

A: BRAIN DERIVED NEUROTROPHIC FACTOR
B: NEUROTROPHIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5026
Polymers54,3824
Non-polymers1202
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-16 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.400, 45.100, 68.000
Angle α, β, γ (deg.)90.00, 118.30, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO B 47

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Components

#1: Protein BRAIN DERIVED NEUROTROPHIC FACTOR / BDNF


Mass: 13534.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SUPPLIED BY REGENERON PHARM.; / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P23560
#2: Protein NEUROTROPHIN 3 / NT3


Mass: 13656.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HETERODIMER / Source: (gene. exp.) Homo sapiens (human) / Description: SUPPLIED BY REGENERON PHARM.; / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P20783
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
210 %(w/v)PEG40001reservoir
310 %(v/v)2-propanol1reservoir
40.1 Msodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 11771 / % possible obs: 93.4 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 11691 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å / % possible obs: 85.6 % / Num. unique obs: 1455 / Rmerge(I) obs: 0.15

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→20 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 11691
Displacement parametersBiso mean: 45.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 4 70 1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.89
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_it4.354.35
X-RAY DIFFRACTIONx_mcangle_it6.656.65
X-RAY DIFFRACTIONx_scbond_it4.354.35
X-RAY DIFFRACTIONx_scangle_it6.656.65
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å / Total num. of bins used: 9 / Num. reflection obs: 1455 / Rfactor all: 0.324

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