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- PDB-6cku: Solution structure of the zebrafish granulin AaE -

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Basic information

Entry
Database: PDB / ID: 6cku
TitleSolution structure of the zebrafish granulin AaE
ComponentsGranulin-AaE
KeywordsSIGNALING PROTEIN / granulin/epithelin module / beta-hairpin stack / progranulins
Function / homology
Function and homology information


skeletal muscle acetylcholine-gated channel clustering / axon extension / liver development / extracellular region / plasma membrane
Similarity search - Function
Granulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / molecular dynamics
AuthorsWang, P. / Ni, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 141019-97 Canada
CitationJournal: Protein Sci. / Year: 2018
Title: Structure dissection of zebrafish progranulins identifies a well-folded granulin/epithelin module protein with pro-cell survival activities.
Authors: Wang, P. / Chitramuthu, B. / Bateman, A. / Bennett, H.P.J. / Xu, P. / Ni, F.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: 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: Granulin-AaE


Theoretical massNumber of molelcules
Total (without water)5,6981
Polymers5,6981
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 16target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Granulin-AaE


Mass: 5698.431 Da / Num. of mol.: 1 / Fragment: residues 793-848
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: grna / Production host: Escherichia coli (E. coli) / References: UniProt: Q8QGN9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic22D 1H-1H NOESY
142anisotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM zebrafish granulin AaE, 150 mM sodium chloride and 0.2mM EDTA pH 6.8 90%, H2O/10% D2OThe sample was dissolved in 450uL of 10% D2O and 90% NMR Buffer that contains 10mM sodium phosphate, 150 mM sodium chloride and 0.2mM EDTA pH 6.8unlabel_AaE90% H2O/10% D2O
solution20.5 mM [U-15N] zebrafish granulin AaE, 10mM sodium phosphate, 150 mM sodium chloride and 0.2mM EDTA pH 6.8, 90% H2O/10% D2OThe sample was dissolved in 450uL of 10% D2O and 90% NMR Buffer that contains 10mM sodium phosphate, 150 mM sodium chloride and 0.2mM EDTA pH 6.815N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMzebrafish granulin AaEnatural abundance1
0.5 mMzebrafish granulin AaE[U-15N]2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.8 / Pressure: 760 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger et al.refinement
ARIANilges et al.refinement
NMRViewJohnson et al.chemical shift assignment
NMRViewJohnson et al.peak picking
CNS1Brunger et al.structure calculation
ARIANilges et al.structure calculation
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 16 / Conformers submitted total number: 16

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