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- PDB-7sjl: Solution NMR Structure of Immunoglobulin-like Domain of Human Neu... -

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Basic information

Entry
Database: PDB / ID: 7sjl
TitleSolution NMR Structure of Immunoglobulin-like Domain of Human Neuregulin-1
ComponentsNeuregulin-1
KeywordsSUGAR BINDING PROTEIN / HEPARAN-SULFATE BINDING
Function / homology
Function and homology information


ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation / negative regulation of secretion / animal organ development / endocardial cell differentiation ...ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation / negative regulation of secretion / animal organ development / endocardial cell differentiation / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / neural crest cell development / cardiac muscle cell myoblast differentiation / cell communication / PI3K events in ERBB4 signaling / cardiac muscle cell differentiation / mammary gland development / chemorepellent activity / ventricular trabecula myocardium morphogenesis / ErbB-3 class receptor binding / regulation of postsynaptic neurotransmitter receptor internalization / activation of transmembrane receptor protein tyrosine kinase activity / ERBB signaling pathway / negative regulation of cardiac muscle cell apoptotic process / ERBB2 Activates PTK6 Signaling / transmembrane receptor protein tyrosine kinase activator activity / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / Long-term potentiation / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / SHC1 events in ERBB4 signaling / Nuclear signaling by ERBB4 / positive regulation of cardiac muscle cell proliferation / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / GRB2 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / activation of protein kinase B activity / SHC1 events in ERBB2 signaling / cytokine activity / transcription coregulator activity / Signaling by ERBB2 TMD/JMD mutants / growth factor activity / wound healing / positive regulation of protein-containing complex assembly / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / cell population proliferation / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / cell differentiation / intracellular signal transduction / apical plasma membrane / signaling receptor binding / negative regulation of DNA-templated transcription / glutamatergic synapse / positive regulation of cell population proliferation / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Neuregulin, C-terminal / Neuregulin-1 / Neuregulin / Neuregulin intracellular region / EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. ...Neuregulin, C-terminal / Neuregulin-1 / Neuregulin / Neuregulin intracellular region / EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Pro-neuregulin-1, membrane-bound isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsEletsky, A. / Kim, Y. / Rogals, M.J. / Prestegard, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127267 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM134335 United States
CitationJournal: Commun Biol / Year: 2022
Title: Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling
Authors: Khaje, N.A. / Eletsky, A. / Biehn, S.E. / Mobley, C.K. / Rogals, M.J. / Kim, Y. / Mishra, S.K. / Doerksen, R.J. / Lindert, S. / Prestegard, J.H. / Sharp, J.S.
History
DepositionOct 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: Neuregulin-1


Theoretical massNumber of molelcules
Total (without water)13,3501
Polymers13,3501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Neuregulin-1 / Acetylcholine receptor-inducing activity / ARIA / Breast cancer cell differentiation factor p45 / ...Acetylcholine receptor-inducing activity / ARIA / Breast cancer cell differentiation factor p45 / Glial growth factor / Heregulin / HRG / Neu differentiation factor / Sensory and motor neuron-derived factor


Mass: 13350.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRG1, GGF, HGL, HRGA, NDF, SMDF / Plasmid: pET-21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02297

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C CT-HSQC aliphatic
131isotropic12D 1H-13C CT-HSQC aromatic
141isotropic13D (HACA)CONH
151isotropic13D HN(CA)CB
191isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-COSY aromatic
171isotropic13D (H)CCH-COSY aliphatic
161isotropic13D (H)CCH-TOCSY aliphatic
1131isotropic13D 1H-13C,15N NOESY
1122isotropic13D HNCO
1112isotropic13D CBCA(CO)NH
2103isotropic12D 1H-13C CT-HSQC methyl

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.0 mM [U-13C; U-15N] NRG1-Ig, 20 mM sodium phosphate, 100 mM sodium chloride, 4 uM DSS, 0.05 % w/w sodium azide, 93% H2O/7% D2ONC_sample193% H2O/7% D2O
solution20.45 mM [U-13C; U-15N] NRG1-Ig, 20 mM sodium phosphate, 100 mM sodium chloride, 4 uM DSS, 0.05 % w/w sodium azide, 93% H2O/7% D2ONC_sample293% H2O/7% D2O
solution30.34 mM [5% 13C; U-15N] NRG1-Ig, 20 mM TRIS, 300 mM sodium chloride, 5 uM DSS, 0.05 % w/w sodium azide, 93% H2O/7% D2ONC5_sample93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMNRG1-Ig[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
4 uMDSSnatural abundance1
0.05 % w/wsodium azidenatural abundance1
0.45 mMNRG1-Ig[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
4 uMDSSnatural abundance2
0.05 % w/wsodium azidenatural abundance2
0.34 mMNRG1-Ig[5% 13C; U-15N]3
20 mMTRISnatural abundance3
300 mMsodium chloridenatural abundance3
5 uMDSSnatural abundance3
0.05 % w/wsodium azidenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMPBS_pH6_56.5 1 atm298 K
2300 mMTRIS_pH7_57.5 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz / Details: 1.7 mm TCI cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
ASDP1Huang, Mao, Xu and Montelionestructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
TopSpin4Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS-NShen and Baxdata analysis
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: refined in explict water bath using PARAM19 force field
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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