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- PDB-2jwn: Solution NMR structure of the protease-resistent domain of Xenopu... -

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Basic information

Entry
Database: PDB / ID: 2jwn
TitleSolution NMR structure of the protease-resistent domain of Xenopus laevis ePABP2
ComponentsEmbryonic polyadenylate-binding protein 2-B
KeywordsRNA BINDING PROTEIN / ePABP2 / poly(A) binding / Structural Genomics / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / Cytoplasm RNA-binding / CESG
Function / homology
Function and homology information


poly(A) binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleus / cytoplasm
Similarity search - Function
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
Embryonic polyadenylate-binding protein 2-B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / Torsion Angle Dynamics, Simulated Annealing
AuthorsSong, J. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural basis for RNA recognition by a type II poly(A)-binding protein.
Authors: Song, J. / McGivern, J.V. / Nichols, K.W. / Markley, J.L. / Sheets, M.D.
History
DepositionOct 16, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: 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_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 1.3May 29, 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: Embryonic polyadenylate-binding protein 2-B
B: Embryonic polyadenylate-binding protein 2-B


Theoretical massNumber of molelcules
Total (without water)27,1032
Polymers27,1032
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 #5lowest energy

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Components

#1: Protein Embryonic polyadenylate-binding protein 2-B / Embryonic poly(A)-binding protein 2-B / Embryonic poly(A)-binding protein type II-B / ePABP2-B / XePABP2-B


Mass: 13551.257 Da / Num. of mol.: 2 / Fragment: Protease-resistent domain: Residues 60-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Tissue: Oocyte / Gene: epabp2-B / Plasmid: PVP56K / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TY21

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
141H(CCO)NH
151CBCA(CO)NH
161C(CO)NH
171HCCHTOCSY
181HBACONH
19113C-EDITED 1H,1H-NOESY
110115C-EDITED 1H,1H-NOESY
111213C,15N filtered, 13C EDITED 1H,1H-NOESY
212315N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] ePABP2-trp, 100 mM NaCl, 10 mM NaAc, 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] ePABP2-trp, 0.5 mM ePABP2-trp, 100 mM NaCl, 10 mM NaAc, 90% H2O, 10% D2O90% H2O/10% D2O
30.5 mM [U-100% 15N] ePABP2-trp, 5 % PEG, 100 mM NaCl, 10 mM NaAc, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMePABP2-trp[U-100% 13C; U-100% 15N]1
100 mMNaCl1
10 mMNaAc1
0.5 mMePABP2-trp-1[U-100% 13C; U-100% 15N]2
0.5 mMePABP2-trp-22
100 mMNaCl2
10 mMNaAc2
0.5 mMePABP2-trp[U-100% 15N]3
5 %PEG3
100 mMNaCl3
10 mMNaAc3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110051 atm308 K
210051 atm302 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.17.0Schwieters, C.D., Kuszewski, J.J., Tjandra, N., Clore, G.M.refinement
XwinNMR3.5Brukercollection
NMRPipe97.027.12.56Delagio, F. et al.processing
Sparky3.113Goddard, T.D. and Kneller, D.G.data analysis
GARANT2.1Bartels, C. et aldata analysis
CYANA2.1Guntert, P. et alstructural calculation
RefinementMethod: Torsion Angle Dynamics, Simulated Annealing / Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 4178 NOE RESTRAINTS (1672 INTRA, 866 SEQUENTIAL, 562 MEDIUM, 912 LONG RANGE INTERMOLECULAR AND 166 INTERMOLECULAR), 116 HBOND RESTRAINTS, 326 PHI AND PSI ...Details: STRUCTURES ARE BASED ON A TOTAL OF 4178 NOE RESTRAINTS (1672 INTRA, 866 SEQUENTIAL, 562 MEDIUM, 912 LONG RANGE INTERMOLECULAR AND 166 INTERMOLECULAR), 116 HBOND RESTRAINTS, 326 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS AND 188 N-H RDC CONSTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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