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- PDB-2cjk: Structure of the RNA binding domain of Hrp1 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 2cjk
TitleStructure of the RNA binding domain of Hrp1 in complex with RNA
Components
  • 5'-R(*UP*AP*UP*AP*UP*AP*UP*AP)-3'
  • NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 4
KeywordsRNA BINDING PROTEIN / HRP1 / RNA-BINDING / RNA PROCESSING / MRNA PROCESSING / NONSENSE-MEDIATED MRNA DECAY / CLEAVAGE / POLYADENYLATION / NUCLEAR PROTEIN / RNA-BINDING PROTEIN
Function / homology
Function and homology information


response to DNA damage checkpoint signaling / mRNA cleavage factor complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / : / mRNA processing / cytoplasmic stress granule / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
HRP1, RNA recognition motif 1 / 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
RNA / Nuclear polyadenylated RNA-binding protein 4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / XPLOR-NIH, CNS
AuthorsPerez-Canadillas, J.M.
CitationJournal: EMBO J. / Year: 2006
Title: Grabbing the message: structural basis of mRNA 3'UTR recognition by Hrp1.
Authors: Perez-Canadillas, J.M.
History
DepositionApr 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 4
B: 5'-R(*UP*AP*UP*AP*UP*AP*UP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)21,5622
Polymers21,5622
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 / 50COMPARISON BETWEEN ENERGY- ORDERED RMSD PROFILES AND TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 4 / HRP1 / CLEAVAGE FACTOR IB / CFIB


Mass: 19065.559 Da / Num. of mol.: 1 / Fragment: RNA-BINDING DOMAIN, RESIDUES 156-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99383
#2: RNA chain 5'-R(*UP*AP*UP*AP*UP*AP*UP*AP)-3' / POLYADENYLATION ENHANCEMENT ELEMENT


Mass: 2496.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-NOESY-HSQC
22113C-NOESY- HSQC
331NOESY
441TOCSY AND COSY
551NOESY
661TOCSY AND COSY
771HNCA
881HN(CO)CA
991CBCACOHN
10101(H)CCH-COSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM6.0 1.0 atm298.0 K
225 mM6.0 1.0 atm298.0 K
325 mM6.0 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance8002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSCHWIETERSrefinement
NMRPIPEstructure solution
ANSIGstructure solution
XWIN-NMRstructure solution
RefinementMethod: XPLOR-NIH, CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: COMPARISON BETWEEN ENERGY- ORDERED RMSD PROFILES AND TOTAL ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 25

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