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- PDB-6yw8: NMR solution structure of unbound recombinant human Nerve Growth ... -

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Basic information

Entry
Database: PDB / ID: 6yw8
TitleNMR solution structure of unbound recombinant human Nerve Growth Factor (rhNGF)
ComponentsBeta-nerve growth factor
KeywordsHORMONE / human NGF / unbound structure / homodimer / cystin-knot
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway ...NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / positive regulation of collateral sprouting / NADE modulates death signalling / Signalling to p38 via RIT and RIN / peripheral nervous system development / ARMS-mediated activation / positive regulation of Ras protein signal transduction / PI3K/AKT activation / regulation of neuron differentiation / Frs2-mediated activation / NRAGE signals death through JNK / extrinsic apoptotic signaling pathway via death domain receptors / Signalling to RAS / positive regulation of DNA binding / cell surface receptor protein tyrosine kinase signaling pathway / p75NTR recruits signalling complexes / positive regulation of neuron differentiation / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / neuron projection morphogenesis / endosome lumen / growth factor activity / modulation of chemical synaptic transmission / memory / Golgi lumen / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron apoptotic process / negative regulation of cell population proliferation / axon / lipid binding / dendrite / positive regulation of gene expression / extracellular space / extracellular region / cytosol
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 cytokine
Similarity search - Domain/homology
Beta-nerve growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGolic Grdadolnik, S. / Paoletti, F.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-8145 Slovenia
Slovenian Research AgencyP1-0010 Slovenia
Slovenian Research AgencyJ1-1705 Slovenia
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions.
Authors: Paoletti, F. / Merzel, F. / Cassetta, A. / Ogris, I. / Covaceuszach, S. / Grdadolnik, J. / Lamba, D. / Golic Grdadolnik, S.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 3, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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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)26,5742
Polymers26,5742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3730 Å2
ΔGint-28 kcal/mol
Surface area14310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

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


Mass: 13287.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: hNGF is a homodimer. It has 3 disulfide bridges per protomer. Chain A: CYS 15 to CYS 80 CYS 58 to CYS 108 CYS 68 to CYS 110 Chain B: Chain A: CYS 15 to CYS 80 CYS 58 to CYS 108 CYS 68 to CYS 110
Source: (gene. exp.) Homo sapiens (human) / Gene: NGF, NGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01138

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
121isotropic12D 1H-15N HSQC
131isotropic13D 1H-15N NOESY
112isotropic13D HNCA
142isotropic12D 1H-13C HSQC aliphatic
152isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.1 mM [U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O0.1 mM [U-99% 15N] Nerve Growth Factor, 50 mM HEPES, pH 7, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMNerve Growth Factor[U-99% 15N]1
50 mMHEPESnatural abundance1
0.1 mMNerve Growth Factor[U-99% 13C; U-99% 15N]2
50 mMHEPESnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: Sample1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.2Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M.refinement
ARIA2.3.2Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M.structure calculation
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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