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- PDB-4cyk: Structural basis for binding of Pan3 to Pan2 and its function in ... -

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Entry
Database: PDB / ID: 4cyk
TitleStructural basis for binding of Pan3 to Pan2 and its function in mRNA recruitment and deadenylation
ComponentsPAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
KeywordsTRANSCRIPTION / PAN3P / PAN2P / POLYA / RNA / DEADENYLATION
Function / homology
Function and homology information


PAN complex / Deadenylation of mRNA / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / postreplication repair / P-body / mRNA processing / protein kinase activity / DNA repair / RNA binding ...PAN complex / Deadenylation of mRNA / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / postreplication repair / P-body / mRNA processing / protein kinase activity / DNA repair / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3160 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Protein kinase domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3160 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PAN2-PAN3 deadenylation complex subunit PAN3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / CNS 1.2
AuthorsWolf, J. / Valkov, E. / Allen, M.D. / Meineke, B. / Gordiyenko, Y. / McLaughlin, S.H. / Olsen, T.M. / Robinson, C.V. / Bycroft, M. / Stewart, M. / Passmore, L.A.
CitationJournal: Embo J. / Year: 2014
Title: Structural Basis for Pan3 Binding to Pan2 and its Function in Mrna Recruitment and Deadenylation.
Authors: Wolf, J. / Valkov, E. / Allen, M.D. / Meineke, B. / Gordiyenko, Y. / Mclaughlin, S.H. / Olsen, T.M. / Robinson, C.V. / Bycroft, M. / Stewart, M. / Passmore, L.A.
History
DepositionApr 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Atomic model
Revision 1.2Jun 4, 2014Group: Atomic model
Revision 1.3Jun 11, 2014Group: Database references
Revision 1.4Jul 30, 2014Group: Database references
Revision 1.5Apr 27, 2016Group: Atomic model / Derived calculations / Other
Revision 1.6Jun 23, 2021Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_exptl_sample_conditions ...pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_representative / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_representative.selection_criteria / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8072
Polymers4,7411
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN3P


Mass: 4741.405 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-41
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PHLTV / Production host: ESCHERICHIA COLI B41 (bacteria) / References: UniProt: P36102
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR AND TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN

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Sample preparation

DetailsContents: 90% WATER / 10% D2O
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE DRXBrukerAVANCE DRX6001
Bruker AVANCE DRXBrukerAVANCE DRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: CNS 1.2 / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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