[English] 日本語
Yorodumi
- PDB-2lxi: NMR structure of the N-terminal RNA Binding domain 1 (RRM1) of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lxi
TitleNMR structure of the N-terminal RNA Binding domain 1 (RRM1) of the protein RBM10 from Homo sapiens
ComponentsRNA-binding protein 10
KeywordsRNA BINDING PROTEIN / RNA binding / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


vascular associated smooth muscle cell apoptotic process / vascular associated smooth muscle cell proliferation / miRNA binding / 3'-UTR-mediated mRNA stabilization / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome ...vascular associated smooth muscle cell apoptotic process / vascular associated smooth muscle cell proliferation / miRNA binding / 3'-UTR-mediated mRNA stabilization / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / nuclear speck / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
RNA-binding protein 10, RNA recognition motif 2 / RBM10, OCRE domain / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others ...RNA-binding protein 10, RNA recognition motif 2 / RBM10, OCRE domain / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RRM (RNA recognition motif) domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / 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-binding protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsSerrano, P. / Geralt, M. / Dutta, S.K. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR structure of the N-terminal RNA Binding domain 1 (RRM1) of the protein RBM10 from Homo sapiens
Authors: Serrano, P. / Wuthrich, K.
History
DepositionAug 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein 10


Theoretical massNumber of molelcules
Total (without water)10,4801
Polymers10,4801
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)19 / 80target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein RNA-binding protein 10 / G patch domain-containing protein 9 / RNA-binding motif protein 10 / RNA-binding protein S1-1 / S1-1


Mass: 10479.848 Da / Num. of mol.: 1 / Fragment: RRM 1 domain residues 128-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM10, DXS8237E, GPATC9, GPATCH9, KIAA0122 / Production host: Escherichia coli (E. coli) / References: UniProt: P98175

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D 1H-15N NOESY
151APSY 4D-HACANH
161APSY 5D-CBCA(CO)NH
171APSY 5D-(HA)CA(CO)NH

-
Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 50 mM sodium chloride, 20 mM sodium phosphate, 5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-98% 13C; U-98% 15N]1
50 mMsodium chloride-21
20 mMsodium phosphate-31
5 mMsodium azide-41
Sample conditionsIonic strength: 0.220 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
OPALpLUGINB, H.L., WUTHRICH, K.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 19

+
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