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- PDB-2jqd: Structure of the Leucine-Rich Repeat domain of LANP -

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Basic information

Entry
Database: PDB / ID: 2jqd
TitleStructure of the Leucine-Rich Repeat domain of LANP
ComponentsAcidic leucine-rich nuclear phosphoprotein 32 family member A
KeywordsGENE REGULATION / PROTEIN BINDING / LANP/Anp32a / LRR domain / phosphoprotein / PP2A inhibitor / tumor suppression / transcriptional regulation / RNA shuttling / apoptosis / cerebellar morphogenesis
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / nucleocytoplasmic transport / nuclear matrix / histone binding / regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Acidic leucine-rich nuclear phosphoprotein 32 family member A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsThe Leucine-Rich Repeat domain (LRR) of Leucine rich Acidic Nuclear Protein (LANP/Anp32a)
Authorsde Chiara, C. / Pastore, A.
Citation
Journal: Febs J. / Year: 2008
Title: Structural bases for recognition of Anp32/LANP proteins
Authors: de Chiara, C. / Menon, R.P. / Pastore, A.
#1: Journal: Cerebellum / Year: 2005
Title: The Anp32 family of proteins containing leucine-rich repeats
Authors: Matilla, A. / Radrizzani, M.
#2: Journal: J.Biomol.Nmr / Year: 2007
Title: NMR assignment of the Leucine-Rich Repeat domain of LANP/Anp32a
Authors: de Chiara, C. / Kelly, G. / Frenkiel, T.A. / Pastore, A.
History
DepositionMay 31, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acidic leucine-rich nuclear phosphoprotein 32 family member A


Theoretical massNumber of molelcules
Total (without water)19,2141
Polymers19,2141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1regularity of secondary sturctures

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Components

#1: Protein Acidic leucine-rich nuclear phosphoprotein 32 family member A / Potent heat-stable protein phosphatase 2A inhibitor I1PP2A / Acidic nuclear phosphoprotein pp32 / ...Potent heat-stable protein phosphatase 2A inhibitor I1PP2A / Acidic nuclear phosphoprotein pp32 / Leucine-rich acidic nuclear protein / PHAPI / MAPM


Mass: 19213.932 Da / Num. of mol.: 1 / Fragment: The N-terminal LRR domain of LANP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anp32a, Anp32, Lanp / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: O35381

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The Leucine-Rich Repeat domain (LRR) of Leucine rich Acidic Nuclear Protein (LANP/Anp32a)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1233D 1H-13C NOESY
1312D J-MODULATED 1H-15N HSQC
1412D J-MODULATED 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-98% 15N] LANP LRR domain, 10 mM TRIS, 2 mM TCEP, 90 % H2O, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-98% 15N] LANP LRR domain, 10 mM TRIS, 2 mM TCEP, 100 % [U-99% 2H] D2O, 0.02 % sodium azide, 100% D2O100% D2O
30.5 mM [U-98% 13C; U-98% 15N] LANP LRR domain, 10 mM TRIS, 2 mM TCEP, 90 % H2O, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLANP LRR domain[U-98% 15N]1
10 mMTRIS1
2 mMTCEP1
90 %H2O1
10 %D2O[U-99% 2H]1
0.02 %sodium azide1
0.5 mMLANP LRR domain[U-98% 15N]2
10 mMTRIS2
2 mMTCEP2
100 %D2O[U-99% 2H]2
0.02 %sodium azide2
0.5 mMLANP LRR domain[U-98% 13C; U-98% 15N]3
10 mMTRIS3
2 mMTCEP3
90 %H2O3
10 %D2O[U-99% 2H]3
0.02 %sodium azide3
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement
NMR representativeSelection criteria: regularity of secondary sturctures
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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