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- PDB-2rqg: Structure of GSPT1/ERF3A-PABC -

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Basic information

Entry
Database: PDB / ID: 2rqg
TitleStructure of GSPT1/ERF3A-PABC
Components
  • G1 to S phase transition 1
  • Polyadenylate-binding protein 1
KeywordsPROTEIN BINDING / PROTEIN-PROTEIN COMPLEX / GTP-binding / Nucleotide-binding / Alternative splicing / Cytoplasm / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation release factor complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / regulation of translational termination ...Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation release factor complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / regulation of translational termination / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / poly(A) binding / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / translation release factor activity / regulatory ncRNA-mediated gene silencing / mRNA stabilization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / poly(U) RNA binding / 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) / translational termination / cytosolic ribosome / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribonucleoprotein complex / focal adhesion / GTPase activity / mRNA binding / GTP binding / RNA binding / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein ...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 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / : / GTP-eEF1A C-terminal domain-like / : / RNA recognition motif domain, eukaryote / RNA recognition motif / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Translation protein, beta-barrel domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyadenylate-binding protein 1 / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsOsawa, M. / Nakanishi, T. / Hosoda, N. / Uchida, S. / Hoshino, T. / Katada, I. / Shimada, I.
CitationJournal: To be Published
Title: Eukaryotic Translation Termination Factor Gspt/Erf3 Recognizes Pabp with Chemical Exchange Using Two Overlapping Motifs
Authors: Osawa, M. / Nakanishi, T. / Hosoda, N. / Uchida, S. / Hoshino, T. / Katada, I. / Shimada, I.
History
DepositionMay 8, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: G1 to S phase transition 1
B: Polyadenylate-binding protein 1


Theoretical massNumber of molelcules
Total (without water)11,1092
Polymers11,1092
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide G1 to S phase transition 1 / GSPT1/eRF3a PAM2-1


Mass: 2112.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 64-82 (UNP residues 15-33)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gspt1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8K2E1, UniProt: Q8R050*PLUS
#2: Protein Polyadenylate-binding protein 1 / Poly(A)-binding protein 1 / PABP 1


Mass: 8996.363 Da / Num. of mol.: 1 / Fragment: PABC DOMAIN
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
111NOESY
1213D 13C-SEPARATED NOESY
131HNHA
14113C-EDITED/13C-FILTERED NOESY
1513D 15N- SEPARATED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] G1 TO S PHASE TRANSITION 1-1, 1 mM [U-98% 13C; U-98% 15N] POLYADENYLATE-BINDING PROTEIN 1-2, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMG1 TO S PHASE TRANSITION 1-1[U-98% 13C; U-98% 15N]1
1 mMPOLYADENYLATE-BINDING PROTEIN 1-2[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 0.15M / pH: 6.5 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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