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- PDB-1s79: Solution structure of the central RRM of human La protein -

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Basic information

Entry
Database: PDB / ID: 1s79
TitleSolution structure of the central RRM of human La protein
ComponentsLupus La protein
KeywordsRNA BINDING PROTEIN / TRANSLATION / RRM / alpha/beta
Function / homology
Function and homology information


nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / IRES-dependent viral translational initiation / RNA Polymerase III Transcription Termination / protein localization to cytoplasmic stress granule / tRNA export from nucleus / tRNA modification / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal ...nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / IRES-dependent viral translational initiation / RNA Polymerase III Transcription Termination / protein localization to cytoplasmic stress granule / tRNA export from nucleus / tRNA modification / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / sequence-specific mRNA binding / poly(U) RNA binding / tRNA processing / positive regulation of translation / cytoplasmic stress granule / tRNA binding / chromosome, telomeric region / ribonucleoprotein complex / mRNA binding / DNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA binding motif / Lupus La protein / xRRM domain profile. / La protein, xRRM domain / 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. / RRM (RNA recognition motif) domain ...RNA binding motif / Lupus La protein / xRRM domain profile. / La protein, xRRM domain / 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. / RRM (RNA recognition motif) domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAlfano, C. / Sanfelice, D. / Babon, J. / Kelly, G. / Jacks, A. / Curry, S. / Conte, M.R.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein.
Authors: Alfano, C. / Sanfelice, D. / Babon, J. / Kelly, G. / Jacks, A. / Curry, S. / Conte, M.R.
#1: Journal: J.Biomol.NMR / Year: 2003
Title: Resonance assignment and secondary structure of an N-terminal fragment of the human La protein
Authors: Alfano, C. / Babon, J. / Kelly, G. / Curry, S. / Conte, M.R.
History
DepositionJan 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lupus La protein


Theoretical massNumber of molelcules
Total (without water)12,1931
Polymers12,1931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Lupus La protein / Sjogren syndrome type B antigen / SS-B / La ribonucleoprotein / La autoantigen


Mass: 12193.004 Da / Num. of mol.: 1 / Fragment: Central RRM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: P05455

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNCA
141HN(CO)CA
151CBCA(CO)NH
161HN(CA)CB

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Sample preparation

DetailsContents: 0.4 mM RRM U-15N,13C; 20mM phosphate buffer, 100mM KCl, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
NMRPipe1Delaglioprocessing
VNMR1cVariancollection
XEASY6600wuthrichdata analysis
MOLMOL2.6wuthichdata analysis
TALOS1999.019.15.47Baxdata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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