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- PDB-2m5w: NMR Solution Structure of the La motif (N-terminal Domain, NTD) o... -

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Basic information

Entry
Database: PDB / ID: 2m5w
TitleNMR Solution Structure of the La motif (N-terminal Domain, NTD) of Dictyostelium discoideum La protein
ComponentsLupus La protein
KeywordsRNA BINDING PROTEIN / Lupus protein / La motif
Function / homology
Function and homology information


RNA processing / phagocytic vesicle / ribonucleoprotein complex / RNA binding / nucleus
Similarity search - Function
RNA binding motif / Lupus La protein / La protein, xRRM domain / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA recognition motif domain ...RNA binding motif / Lupus La protein / La protein, xRRM domain / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA recognition motif domain / RNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH La-type RNA-binding domain-containing protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / molecular dynamics, restrained energy minimization
Model type detailsminimized average
AuthorsVourtsis, D.J. / Chasapis, C.T. / Apostolidi, M. / Stathopoulos, C. / Bentrop, D. / Spyroulias, G.A.
Citation
Journal: To be Published
Title: NMR Solution Structure of the La motif (N-terminal Domain, NTD) of Dictyostelium discoideum La protein
Authors: Vourtsis, D.J. / Chasapis, C.T. / Apostolidi, M. / Stathopoulos, C. / Bentrop, D. / Spyroulias, G.A.
#1: Journal: BIOMOL.NMR ASSIGN.
Title: (1)H, (15)N, (13)C assignment and secondary structure determination of two domains of La protein from D. discoideum.
Authors: Apostolidi, M. / Vourtsis, D.J. / Chasapis, C.T. / Stathopoulos, C. / Bentrop, D. / Spyroulias, G.A.
History
DepositionMar 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)10,5481
Polymers10,5481
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)31 / 31target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Lupus La protein


Mass: 10547.895 Da / Num. of mol.: 1 / Fragment: La-type RNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_0204655, DDB_G0281763 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54TG6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1323D CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HN(CO)CA
1823D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.37 mM [U-98% 15N] La-type RNA-binding domain, 50 mM buffer salts, 90% H2O/10% D2O90% H2O/10% D2O
20.37 mM [U-98% 13C; U-98% 15N] La-type RNA-binding domain, 50 mM buffer salts, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.37 mMLa-type RNA-binding domain-1[U-98% 15N]1
50 mMbuffer salts-21
0.37 mMLa-type RNA-binding domain-3[U-98% 13C; U-98% 15N]2
50 mMbuffer salts-42
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker DPXBrukerDPX4002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichchemical shift assignment
AMBER_5.0Case, D.A. et al.refinement
RefinementMethod: molecular dynamics, restrained energy minimization / Software ordinal: 1
NMR constraintsNOE constraints total: 951 / NOE intraresidue total count: 205 / NOE long range total count: 118 / NOE medium range total count: 223 / NOE sequential total count: 405
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 31 / Conformers submitted total number: 31

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