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- PDB-2k8g: Solution structure of RRM2 domain of PABP1 -

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Basic information

Entry
Database: PDB / ID: 2k8g
TitleSolution structure of RRM2 domain of PABP1
ComponentsPolyadenylate-binding protein 1
KeywordsTRANSLATION / protein / Alternative splicing / Cytoplasm / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / mRNA stabilization / poly(A) binding ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / mRNA stabilization / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / : / cell leading edge / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / lamellipodium / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyadenylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsBarsukov, I. / Parnham, S.
CitationJournal: To be Published
Title: Solution structure of RRM2 domain of PABP1
Authors: Barsukov, I. / Parnham, S. / Norman, J.
History
DepositionSep 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _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 1


Theoretical massNumber of molelcules
Total (without water)10,6261
Polymers10,6261
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)25 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Polyadenylate-binding protein 1 / Poly(A)-binding protein 1 / PABP 1


Mass: 10626.049 Da / Num. of mol.: 1 / Fragment: RRM2 domain (UNP residues 90-182)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11940

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D (H)CCH-TOCSY
1713D 1H-13C NOESY
1823D 1H-15N NOESY
1923D 1H-15N TOCSY
11032D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] PABP1, 20 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 15N] PABP1, 20 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
31 mM PABP1, 20 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPABP1[U-98% 13C; U-98% 15N]1
20 mMsodium chloride1
20 mMsodium phosphate1
1 mMDTT1
1 mMPABP1[U-98% 15N]2
20 mMsodium chloride2
20 mMsodium phosphate2
1 mMDTT2
1 mMPABP13
20 mMsodium chloride3
20 mMsodium phosphate3
1 mMDTT3
Sample conditionsIonic strength: 0.04 / pH: 6.1 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
ARIA1.3Linge, O'Donoghue and Nilgesstructure solution
ARIA1.3Linge, O'Donoghue and Nilgesrefinement
CCPN_Analysis1Vranken, Boucher, Stevens, Fogh, Lauedata analysis
CCPN_Analysis1Vranken, Boucher, Stevens, Fogh, Lauechemical shift assignment
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3584 / NOE intraresidue total count: 1036 / NOE long range total count: 1273 / NOE medium range total count: 547 / NOE sequential total count: 728 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 47 / Protein psi angle constraints total count: 47
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.76 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 7 ° / Maximum upper distance constraint violation: 0.63 Å / Torsion angle constraint violation method: CNS
NMR ensemble rmsDistance rms dev: 0.03 Å / Distance rms dev error: 0.0015 Å

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