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- PDB-6i9b: NMR structure of the La module from human LARP4A -

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Basic information

Entry
Database: PDB / ID: 6i9b
TitleNMR structure of the La module from human LARP4A
ComponentsLa-related protein 4
KeywordsRNA BINDING PROTEIN / La-related proteins / LARPs / PABP-binding protein / La module
Function / homology
Function and homology information


poly(A) binding / regulation of cell morphogenesis / post-transcriptional regulation of gene expression / cytoskeleton organization / mRNA 3'-UTR binding / positive regulation of translation / cytoplasmic stress granule / translation / RNA binding / membrane / cytosol
Similarity search - Function
LARP4, RNA recognition motif / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
La-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsConte, M.R. / Martino, L. / Atkinson, R.A. / Kelly, G. / Cruz-Gallardo, I. / De Tito, S. / Trotta, R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Royal SocietyNF140482 United Kingdom
European Molecular Biology OrganizationALT400-2010 United Kingdom
European Commission655341 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA.
Authors: Cruz-Gallardo, I. / Martino, L. / Kelly, G. / Atkinson, R.A. / Trotta, R. / De Tito, S. / Coleman, P. / Ahdash, Z. / Gu, Y. / Bui, T.T.T. / Conte, M.R.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 13, 2022Group: Data collection / Database references / Structure summary
Category: audit_author / database_2 / pdbx_nmr_spectrometer
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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: La-related protein 4


Theoretical massNumber of molelcules
Total (without water)20,5771
Polymers20,5771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SAXS, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein La-related protein 4 / La ribonucleoprotein domain family member 4


Mass: 20576.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP4, PP13296 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II / References: UniProt: Q71RC2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-13C HSQC
121isotropic33D 1H-15N NOESY
132isotropic23D 1H-13C NOESY
141isotropic32D 1H-15N HSQC
152isotropic23D 1H-13C NOESY aliphatic
162isotropic13D 1H-13C NOESY aromatic
172isotropic13D (H)CCH-TOCSY
182isotropic13D HNCA
1122isotropic13D HN(CO)CA
1112isotropic23D HN(CA)CB
1102isotropic23D CBCA(CO)NH
192isotropic13D HNCO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1400 uM [U-99% 15N] RNA binding protein, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution2400 uM [U-99% 13C; U-99% 15N] RNA binding protein, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMRNA binding protein[U-99% 15N]1
400 uMRNA binding protein[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 100 mM KCl mM / Label: conditions_1 / pH: 7.25 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE9503

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
CcpNmr AnalysisCCPNchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxgeometry optimization
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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