[English] 日本語
Yorodumi
- PDB-2mqp: Structural Investigation of hnRNP L bound to RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mqp
TitleStructural Investigation of hnRNP L bound to RNA
Components
  • Protein Hnrnpl
  • RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / Protein-RNA Complex / RRM / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA CDS binding / ribonucleoprotein granule / response to peptide / pronucleus / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / pre-mRNA intronic binding ...Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA CDS binding / ribonucleoprotein granule / response to peptide / pronucleus / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / pre-mRNA intronic binding / cellular response to amino acid starvation / positive regulation of translation / mRNA 3'-UTR binding / mRNA processing / circadian rhythm / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / mRNA binding / synapse / chromatin / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / RRM domain / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RRM (RNA recognition motif) domain ...hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / RRM domain / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / 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 / Heterogeneous nuclear ribonucleoprotein L / Heterogeneous nuclear ribonucleoprotein L
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsBlatter, M. / Allain, F.
CitationJournal: To be Published
Title: Structural Investigation of hnRNP L bound to RNA
Authors: Blatter, M. / Allain, F.
History
DepositionJun 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.db_id / _pdbx_database_related.db_name
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: Protein Hnrnpl
B: RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)14,9382
Polymers14,9382
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 / 250structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Protein Hnrnpl


Mass: 13079.706 Da / Num. of mol.: 1 / Fragment: unp residues 174-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hnrnpl / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z3R2, UniProt: F1LQ48*PLUS
#2: RNA chain RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')


Mass: 1858.205 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Second RNA Recognition Motif Domain of hnRNP L bound to ACACAC RNA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY aliphatic
1323D 1H-13C NOESY aromatic
1432D 1H-1H NOESY
1532D 1H-1H TOCSY
1643D F3-filtered-F2-edited NOESY
1742D F2-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-100% 15N] protein_1, 2 mM RNA (5'-R(*AP*CP*AP*CP*AP*C)-3'), 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-100% 13C; U-100% 15N] protein_1, 2 mM RNA (5'-R(*AP*CP*AP*CP*AP*C)-3'), 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
32 mM [U-100% 15N] protein_1, 2 mM protein_1, 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
42 mM [U-100% 13C; U-100% 15N] protein_1, 2 mM RNA (5'-R(*AP*CP*AP*CP*AP*C)-3'), 60 mM sodium chloride, 40 mM sodium phosphate, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity_1-1[U-100% 15N]1
2 mMRNA (5'-R(*AP*CP*AP*CP*AP*C)-3')-21
60 mMsodium chloride-31
40 mMsodium phosphate-41
1 mMDTT-51
2 mMentity_1-6[U-100% 13C; U-100% 15N]2
2 mMRNA (5'-R(*AP*CP*AP*CP*AP*C)-3')-72
60 mMsodium chloride-82
40 mMsodium phosphate-92
1 mMDTT-102
2 mMentity_1-11[U-100% 15N]3
2 mMentity_1-123
60 mMsodium chloride-133
40 mMsodium phosphate-143
1 mMDTT-153
2 mMentity_1-16[U-100% 13C; U-100% 15N]4
2 mMRNA (5'-R(*AP*CP*AP*CP*AP*C)-3')-174
60 mMsodium chloride-184
40 mMsodium phosphate-194
1 mMDTT-204
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 310.15 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / 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