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- PDB-5lsd: recombinant mouse Nerve Growth Factor -

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Basic information

Entry
Database: PDB / ID: 5lsd
Titlerecombinant mouse Nerve Growth Factor
ComponentsBeta-nerve growth factor
KeywordsCELL CYCLE / NGF / homodimer / cystin-knot / dimerfit_1
Function / homology
Function and homology information


TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation / nerve growth factor receptor binding / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / Retrograde neurotrophin signalling / NF-kB is activated and signals survival / metalloendopeptidase inhibitor activity / positive regulation of neuron maturation / regulation of neurotransmitter secretion / nerve growth factor signaling pathway / nerve development / positive regulation of collateral sprouting / peripheral nervous system development / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / regulation of neuron differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of stem cell proliferation / positive regulation of DNA binding / positive regulation of axon extension / positive regulation of protein autophosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / sensory perception of pain / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of neuron differentiation / adult locomotory behavior / neuron projection morphogenesis / positive regulation of protein ubiquitination / endosome lumen / growth factor activity / modulation of chemical synaptic transmission / memory / positive regulation of neuron projection development / circadian rhythm / neuron projection development / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / axon / lipid binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region
Similarity search - Function
Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / 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 ...Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / 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
Beta-nerve growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsPaoletti, F. / de Chiara, C. / Kelly, G. / Lamba, D. / Cattaneo, A. / Pastore, A.
Funding support Italy, 2items
OrganizationGrant numberCountry
European Community Seventh Framework ProgramPaincage Grant number 603191 Italy
MIURPRIN #2010N8PBAA_006 Italy
CitationJournal: Front Mol Biosci / Year: 2016
Title: Conformational Rigidity within Plasticity Promotes Differential Target Recognition of Nerve Growth Factor.
Authors: Paoletti, F. / de Chiara, C. / Kelly, G. / Covaceuszach, S. / Malerba, F. / Yan, R. / Lamba, D. / Cattaneo, A. / Pastore, A.
History
DepositionAug 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-nerve growth factor
B: Beta-nerve growth factor


Theoretical massNumber of molelcules
Total (without water)26,5542
Polymers26,5542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3300 Å2
ΔGint-21 kcal/mol
Surface area13990 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Beta-nerve growth factor / Beta-NGF


Mass: 13277.009 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NGF is a homodimer / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngf, Ngfb / Production host: Escherichia coli (E. coli) / References: UniProt: P01139

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic43D HNCA
1111isotropic42D 1H-15N HSQC
121isotropic43D HNCO
131isotropic43D HN(CA)CB
141isotropic43D 1H-15N NOESY
251isotropic23D 1H-15N NOESY
1121isotropic22D 1H-13C HSQC aliphatic
161isotropic23D 1H-13C NOESY aliphatic
271isotropic53D 1H-13C NOESY aliphatic
2131isotropic52D 1H-13C HSQC aliphatic
181isotropic43D CBCA(CO)NH
191isotropic23D (H)CCH-TOCSY
1101isotropic22D 1H-13C HSQC aromatic
1141isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM sodium phosphate, 1 mM EDTA, 93% H2O/7% D2O
Label: 15N_13C-NGF / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMNerve Growth Factor[U-99% 13C; U-99% 15N]1
50 mMsodium phosphatenatural abundance1
1 mMEDTAnatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM15N_13C-NGF_30deg7 1 atm303 K
250 mM15N_13C-NGF_35deg7 1 atm308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Bruker AVANCEBrukerAVANCE6003
Bruker AVANCEBrukerAVANCE7004
Bruker AVANCEBrukerAVANCE8005

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
ARIA2.3.2Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M. (2007) ARIA2: automated NOE assignment and data integration in NMR structure calculation Bioinformatics 23:381-382refinement
ARIA2.3.2Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M. (2007) ARIA2: automated NOE assignment and data integration in NMR structure calculation Bioinformatics 23:381-382structure calculation
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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