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- PDB-1b98: NEUROTROPHIN 4 (HOMODIMER) -

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Basic information

Entry
Database: PDB / ID: 1b98
TitleNEUROTROPHIN 4 (HOMODIMER)
ComponentsPROTEIN (NEUROTROPHIN-4)
KeywordsHORMONE/GROWTH FACTOR / TARGET-DERIVED SURVIVAL FACTOR / NEUROTROPHIN 4 / NEUROTROPHIN 5 / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


taste bud development / sensory organ boundary specification / ganglion mother cell fate determination / NTF4 activates NTRK2 (TRKB) signaling / Activated NTRK2 signals through PLCG1 / nerve growth factor receptor binding / mechanoreceptor differentiation / nerve growth factor signaling pathway / nerve development / innervation ...taste bud development / sensory organ boundary specification / ganglion mother cell fate determination / NTF4 activates NTRK2 (TRKB) signaling / Activated NTRK2 signals through PLCG1 / nerve growth factor receptor binding / mechanoreceptor differentiation / nerve growth factor signaling pathway / nerve development / innervation / peripheral nervous system development / Activated NTRK2 signals through PI3K / regulation of neuron differentiation / Activated NTRK2 signals through RAS / epidermis development / Activated NTRK2 signals through FRS2 and FRS3 / long-term memory / cell surface receptor protein tyrosine kinase signaling pathway / adult locomotory behavior / neuron projection morphogenesis / growth factor activity / modulation of chemical synaptic transmission / memory / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron apoptotic process / axon / dendrite / extracellular space / extracellular region
Similarity search - Function
Neurotrophin-4 / 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) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...Neurotrophin-4 / 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) / 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: 2.75 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/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 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (NEUROTROPHIN-4)
M: PROTEIN (NEUROTROPHIN-4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9253
Polymers27,8892
Non-polymers351
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-31 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 50.800, 53.000
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein PROTEIN (NEUROTROPHIN-4) / NT4


Mass: 13944.647 Da / Num. of mol.: 2 / Fragment: precursor residues 81-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SUPPLIED BY REGENERON PHARMACUTICALS / Production host: Escherichia coli (E. coli) / References: UniProt: P34130
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growpH: 6.5 / Details: PEG 8000, PIPES, pH 6.50
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: SSRL / Beamline: BL1-5 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD
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: 93 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.031
Reflection
*PLUS
Highest resolution: 2.35 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NT4

Resolution: 2.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.336 -5 %RANDOM
Rwork0.235 ---
obs0.235 8334 93 %-
Displacement parametersBiso mean: 46.3 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 1 49 1671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.048
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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