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- PDB-1jgn: Solution structure of the C-terminal PABC domain of human poly(A)... -

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Basic information

Entry
Database: PDB / ID: 1jgn
TitleSolution structure of the C-terminal PABC domain of human poly(A)-binding protein in complex with the peptide from Paip2
Components
  • polyadenylate-binding protein 1
  • polyadenylate-binding protein-interacting protein 2
KeywordsRNA BINDING PROTEIN / all-helical domain / protein-peptide complex
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 / M-decay: degradation of maternal mRNAs by maternally stored factors / 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 / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / regulation of long-term synaptic potentiation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / cell leading edge / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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) / translation repressor activity / negative regulation of translational initiation / catalytic step 2 spliceosome / mRNA regulatory element binding translation repressor activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / memory / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / lamellipodium / spermatogenesis / negative regulation of translation / translation / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Polyadenylate-binding protein-interacting protein 2-like / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / 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 ...Polyadenylate-binding protein-interacting protein 2-like / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / 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 1 / Polyadenylate-binding protein-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Siddiqui, N. / Coillet-Matillon, S. / Ekiel, I. / Gehring, K.
Citation
Journal: EMBO J. / Year: 2004
Title: Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase
Authors: Kozlov, G. / De Crescenzo, G. / Lim, N.S. / Siddiqui, N. / Fantus, D. / Kahvejian, A. / Trempe, J.F. / Elias, D. / Ekiel, I. / Sonenberg, N. / O'Connor-McCourt, M. / Gehring, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure and function of the C-terminal PABC domain of human poly(A)-binding protein
Authors: Kozlov, G. / Trempe, J.F. / Khaleghpour, K. / Kahvejian, A. / Ekiel, I. / Gehring, K.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: polyadenylate-binding protein 1
B: polyadenylate-binding protein-interacting protein 2


Theoretical massNumber of molelcules
Total (without water)12,7392
Polymers12,7392
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)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein polyadenylate-binding protein 1 / PABP1


Mass: 10347.936 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: P11940
#2: Protein/peptide polyadenylate-binding protein-interacting protein 2 / PAIP2


Mass: 2390.755 Da / Num. of mol.: 1 / Fragment: C-terminal 22 residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: Q9BPZ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 15N-separated NOESY
1443D 13C-separated NOESY
1552D NOESY
1662D NOESY
NMR detailsText: The structure was determined using standard triple-resonance and homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM 15N-labeled PABC; 4mM unlabeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.390% H2O/10% D2O
23mM 15N,13C-labeled PABC; 4mM unlabeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.3100% D2O
32.5mM 15N-labeled peptide; 3mM unlabeled PABC; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.390% H2O/10% D2O
42mM 15N,13C-labeled peptide; 3mM unlabeled PABC; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.3100% D2O
53mM unlabeled PABC; 3mM unlabeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.390% H2O/10% D2O
63mM unlabeled PABC; 3mM unlabeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.3100% D2O
Sample conditionsIonic strength: 0.1M NaCl / 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
Varian UNITYPLUSVarianUNITYPLUS8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker Spectrospincollection
Gifa4.31Delsucprocessing
XEASY1.3.13Wuthrichdata analysis
ARIA0.9Nilgesstructure solution
CNS0.9Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 2058 non-redundant NOE-derived distance constraints, 106 dihedral angle restraints, and 35 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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