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- PDB-1ifw: SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1ifw
TitleSOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEIN FROM SACCHAROMYCES CEREVISIAE
ComponentsPOLYADENYLATE-BINDING PROTEIN, CYTOPLASMIC AND NUCLEAR
KeywordsRNA BINDING PROTEIN / all-helical domain
Function / homology
Function and homology information


regulation of nuclear-transcribed mRNA poly(A) tail shortening / ribonuclease inhibitor activity / poly(A) binding / poly(U) RNA binding / regulation of translational initiation / Translation initiation complex formation / intracellular non-membrane-bounded organelle / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression ...regulation of nuclear-transcribed mRNA poly(A) tail shortening / ribonuclease inhibitor activity / poly(A) binding / poly(U) RNA binding / regulation of translational initiation / Translation initiation complex formation / intracellular non-membrane-bounded organelle / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA transport / molecular condensate scaffold activity / mRNA 3'-UTR binding / promoter-specific chromatin binding / mRNA processing / cytoplasmic stress granule / ribosome / ribonucleoprotein complex / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain ...c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyadenylate-binding protein, cytoplasmic and nuclear
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Siddiqui, N. / Coillet-Matillon, S. / Sprules, T. / Ekiel, I. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Solution structure of the orphan PABC domain from Saccharomyces cerevisiae poly(A)-binding protein.
Authors: Kozlov, G. / Siddiqui, N. / Coillet-Matillon, S. / Trempe, J.F. / Ekiel, I. / Sprules, T. / Gehring, K.
History
DepositionApr 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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: POLYADENYLATE-BINDING PROTEIN, CYTOPLASMIC AND NUCLEAR


Theoretical massNumber of molelcules
Total (without water)10,4451
Polymers10,4451
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)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein POLYADENYLATE-BINDING PROTEIN, CYTOPLASMIC AND NUCLEAR / POLYADENYLATE TAIL-BINDING PROTEIN


Mass: 10445.410 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (490-576)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAB1 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: P04147

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1333D 15N-separated NOESY
1443D 13C-separated NOESY
NMR detailsText: The structure was determined using standard triple-resonance and homonuclear techniques. The N-terminal sequence GPLGS is a cloning artifact.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM protein, 50mM phosphate buffer, 0.1M NaCl, 1mM NaN390% H2O/10% D2O
23mM protein, 50mM phosphate buffer, 0.1M NaCl, 1mM NaN3100% D2O
33mM protein U-15N, 50mM phosphate buffer, 0.1M NaCl, 1mM NaN390% H2O/10% D2O
43mM protein U-15N,13C, 50mM phosphate buffer, 0.1M NaCl, 1mM NaN3100% D2O
Sample conditionsIonic strength: 0.2 / pH: 6.3 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX5001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
Gifa4.31Delsucprocessing
XEASY1.3.13Wuthrichdata analysis
CNS0.9Brungerstructure solution
ARIA0.9Nilgesstructure solution
CNS0.9Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 972 NOE distance constraints, 69 dihedral angles constraints and 40 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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