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- PDB-2kt5: RRM domain of mRNA export adaptor REF2-I bound to HSV-1 ICP27 peptide -

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Basic information

Entry
Database: PDB / ID: 2kt5
TitleRRM domain of mRNA export adaptor REF2-I bound to HSV-1 ICP27 peptide
Components
  • ICP27
  • RNA and export factor-binding protein 2
KeywordsRNA Binding Protein / Viral Protein / REF ICP27 HSV-1 / Chaperone / mRNA processing / mRNA splicing / mRNA transport / Nucleus / RNA-binding / Spliceosome / Transport / RNA Binding Protein - Viral Protein complex
Function / homology
Function and homology information


negative regulation of viral transcription / negative regulation of viral genome replication / mRNA transport / RNA splicing / protein export from nucleus / spliceosomal complex / regulation of protein stability / mRNA processing / single-stranded DNA binding / nucleic acid binding ...negative regulation of viral transcription / negative regulation of viral genome replication / mRNA transport / RNA splicing / protein export from nucleus / spliceosomal complex / regulation of protein stability / mRNA processing / single-stranded DNA binding / nucleic acid binding / host cell cytoplasm / regulation of DNA-templated transcription / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Herpes viral adaptor, REF-binding domain / Herpes viral adaptor-to-host cellular mRNA binding domain / 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 ...Herpes viral adaptor, REF-binding domain / Herpes viral adaptor-to-host cellular mRNA binding domain / 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
ICP27 / Aly/REF export factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsTunnicliffe, N.B. / Golovanov, A.P. / Wilson, S.A. / Hautbergue, G.M.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structural Basis for the Recognition of Cellular mRNA Export Factor REF by Herpes Viral Proteins HSV-1 ICP27 and HVS ORF57.
Authors: Tunnicliffe, R.B. / Hautbergue, G.M. / Kalra, P. / Jackson, B.R. / Whitehouse, A. / Wilson, S.A. / Golovanov, A.P.
History
DepositionJan 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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: ICP27


Theoretical massNumber of molelcules
Total (without water)17,8652
Polymers17,8652
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA and export factor-binding protein 2


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) / Gene: Refbp2, Ref2 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RP / References: UniProt: Q9JJW6
#2: Protein/peptide ICP27


Mass: 4268.931 Da / Num. of mol.: 1 / Fragment: REF interaction fragment, residues 103-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RP / References: UniProt: Q9J0X9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131filtered 13C-NOESY
142filtered 13C-NOESY
1523D 13C-separated NOESY
1623D 15N-separated NOESY
1713D Standard triple-resonance
1823d Standard triple-resonance

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] REF 54-155, 2 mM ICP27 103-138, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] ICP27 103-138, 2 mM REF 54-155, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMREF 54-155[U-99% 13C; U-99% 15N]1
2 mMICP27 103-1381
1 mMICP27 103-138[U-99% 13C; U-99% 15N]2
2 mMREF 54-1552
Sample conditionsIonic strength: 50 / pH: 6.2 / Pressure: AMBIENT bar / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker Avance II+BrukerAVANCE II7002
Varian INOVAVarianINOVA8003

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Processing

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

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