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- PDB-2yka: RRM domain of mRNA export adaptor REF2-I bound to HVS ORF57 peptide -

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Basic information

Entry
Database: PDB / ID: 2yka
TitleRRM domain of mRNA export adaptor REF2-I bound to HVS ORF57 peptide
Components
  • 52 KDA IMMEDIATE-EARLY PHOSPHOPROTEIN
  • RNA AND EXPORT FACTOR-BINDING PROTEIN 2
KeywordsRNA BINDING PROTEIN/TRANSCRIPTION / RNA BINDING PROTEIN-TRANSCRIPTION COMPLEX / RNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA transport / RNA splicing / spliceosomal complex / mRNA processing / single-stranded DNA binding / molecular adaptor activity / host cell cytoplasm / regulation of DNA-templated transcription / host cell nucleus / RNA binding ...mRNA transport / RNA splicing / spliceosomal complex / mRNA processing / single-stranded DNA binding / molecular adaptor activity / host cell cytoplasm / regulation of DNA-templated transcription / host cell nucleus / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / 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
mRNA export factor ICP27 homolog / Aly/REF export factor 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SAIMIRIINE HERPESVIRUS 2 (Herpesvirus saimiri)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTunnicliffe, R.B. / Hautbergue, G.M. / Kalra, P. / Wilson, S.A. / Golovanov, A.P.
CitationJournal: Plos Pathog. / Year: 2014
Title: Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri Orf57 to the Mammalian Export Adaptor Alyref.
Authors: Tunnicliffe, R.B. / Hautbergue, G.M. / Wilson, S.A. / Kalra, P. / Golovanov, A.P.
History
DepositionMay 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 2.0May 15, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA AND EXPORT FACTOR-BINDING PROTEIN 2
B: 52 KDA IMMEDIATE-EARLY PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)16,1042
Polymers16,1042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein RNA AND EXPORT FACTOR-BINDING PROTEIN 2 / REF2-I


Mass: 13596.133 Da / Num. of mol.: 1 / Fragment: RRM DOMAIN, RESIDUES 53-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RP / References: UniProt: Q9JJW6
#2: Protein/peptide 52 KDA IMMEDIATE-EARLY PHOSPHOPROTEIN / ORF57 PROTEIN


Mass: 2507.809 Da / Num. of mol.: 1 / Fragment: RESIDUES 103-120
Source method: isolated from a genetically manipulated source
Details: REF/ALY INTERACTION FRAGMENT OF ORF57 PROTEIN
Source: (gene. exp.) SAIMIRIINE HERPESVIRUS 2 (Herpesvirus saimiri)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RP / References: UniProt: P13199
Sequence detailsREF2-I RESIDUES 54-155. N-TERMINAL SEQUENCE MASMTGGQQMGRDP AND C-TERMINAL LEHHHHHH FROM CLONING. ...REF2-I RESIDUES 54-155. N-TERMINAL SEQUENCE MASMTGGQQMGRDP AND C-TERMINAL LEHHHHHH FROM CLONING. HVS ORF57 RESIDUES 103-120. N-TERMINAL SEQUENCE GPLGS FROM CLONING.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121HNCA
131CBCA(CO)NH
141HN(CA)CB
151HNCO
161HN(CA)CO
171TOCSY-HSQC
181HBHA(CO)NH
191(H)CCH-TOCSY
1101CCH-TOCSY
1111NOESY-HSQC HSQC
1121HNCA
1131CBCA(CO)NH
1141HN(CA)CB
1151HNCO
1161TOCSY- HSQC
1171HBHA(CO)NH
1181NOESY- HSQC
1191FILTERED 13C- NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.2 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P. GUNTERT ET AL.refinement
CYANA2.1structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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