[English] 日本語
Yorodumi
- PDB-2yka: RRM domain of mRNA export adaptor REF2-I bound to HVS ORF57 peptide -

+
Open data


ID or keywords:

Loading...

-
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


viral mRNA export from host cell nucleus / transcription export complex / C5-methylcytidine-containing RNA reader activity / regulation of DNA recombination / RNA export from nucleus / positive regulation of DNA-templated transcription, elongation / replication fork processing / mRNA transport / mRNA export from nucleus / catalytic step 2 spliceosome ...viral mRNA export from host cell nucleus / transcription export complex / C5-methylcytidine-containing RNA reader activity / regulation of DNA recombination / RNA export from nucleus / positive regulation of DNA-templated transcription, elongation / replication fork processing / mRNA transport / mRNA export from nucleus / catalytic step 2 spliceosome / RNA splicing / mRNA processing / single-stranded DNA binding / host cell cytoplasm / molecular adaptor activity / mRNA binding / host cell nucleus / regulation of DNA-templated transcription / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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.

-
Experimental details

-
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

-
Sample preparation

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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more