[English] 日本語
Yorodumi
- PDB-8bgf: NMR solution structure of the N-terminal RRM and flanking linker ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bgf
TitleNMR solution structure of the N-terminal RRM and flanking linker regions of Polypyrimidine tract binding protein 1 using the CYANA CONSENSUS method.
ComponentsPolypyrimidine tract-binding protein 1
KeywordsRNA BINDING PROTEIN / RNA BINDING PROTEIN Alternative splicing repressor IRES trans-acting factor RNA recognition motif Dynamic structure
Function / homology
Function and homology information


negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing ...negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / : / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP 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
Similarity search - Domain/homology
Polypyrimidine tract-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDamberger, F.D. / Beusch, I. / Allain, F.H.-T.
Funding support Switzerland, India, Czech Republic, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation133134 Switzerland
Council of Scientific & Industrial Research (CSIR)CSC0405 India
Czech Science Foundation20-16554S Czech Republic
Citation
Journal: To Be Published
Title: N-terminal domain of Polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition
Authors: Damberger, F. / Krepl, M. / Beusch, I. / Dorn, G. / Maris, C. / Sponer, J. / Ravindranathan, S. / Allain, F.H.-T.
#1: Journal: Nucleic Acids Res / Year: 2020
Title: A transient alpha-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure.
Authors: Maris, C. / Jayne, S. / Damberger, F.F. / Beusch, I. / Dorn, G. / Ravindranathan, S. / Allain, F.H.
History
DepositionOct 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polypyrimidine tract-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,3751
Polymers13,3751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000structures with the least restraint violations
RepresentativeModel #1target function

-
Components

#1: Protein Polypyrimidine tract-binding protein 1 / PTB / 57 kDa RNA-binding protein PPTB-1 / Heterogeneous nuclear ribonucleoprotein I / hnRNP I


Mass: 13375.167 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTBP1, PTB / Plasmid: pTYB11
Details (production host): gene for construct inserted between the NdeI and Xho1 sites
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon-plus RIL / References: UniProt: P26599

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY
231isotropic315N T1-relaxation-15HSQC
241isotropic315N T2-relaxation-T1rho-15NHSQC
251isotropic3{1H}15N-NOE-15NHSQC
161isotropic2relaxation-compensated IzNz Rex HSQC
171isotropic215N T2-relaxation-dispersion CPMG-15NHSQC
181isotropic115N T2-relaxation-dispersion-CPMG-15NHSQC
3173isotropic215N T2-relaxation-dispersion-CPMG-15NHSQC
1181isotropic2cross-correlated DD/CSA relaxation-15NHSQC
NMR detailsText: STRUCTURE WAS CALCULATED USING CONSENSUS METHOD (BUCHNER L AND GUENTERT P 2015 STRUCTURE 23, 425-434). 20 INDEPENDENT STRUCTURE CALCULATIONS OF 100 CONFORMERS WERE PERFORMED AND A SET OF ...Text: STRUCTURE WAS CALCULATED USING CONSENSUS METHOD (BUCHNER L AND GUENTERT P 2015 STRUCTURE 23, 425-434). 20 INDEPENDENT STRUCTURE CALCULATIONS OF 100 CONFORMERS WERE PERFORMED AND A SET OF CONSTRAINTS CONSISTENT AMONG 60% OF THE ENSEMBLES WAS COMBINED FOR A FINAL CONSENSUS CALCULATION TO GENERATE THIS ENSEMBLE THE PROTEIN CONTAINS A DYNAMIC REGION WITH RESIDUAL STRUCTURE. DUE TO THE AMBIGUOUS NATURE OF THE CONSTRAINTS AND THE DYNAMIC REGION NO ENERGY REFINEMENT WAS PERFORMED

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2OWT_15N_protein90% H2O/10% D2O
solution20.8 mM [U-13C,15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2OWT_13C15N_protein90% H2O/10% D2O
solution30.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2OL151G_mutant_15N_protein90% H2O/10% D2O
solution50.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 0.8 mM [U-13C,15N]-99% UCUUU-SL-RNA, 90% H2O/10% D2OWT_15N_protein_13C15N_RNAcomplex90% H2O/10% D2O1:1 complex of 15N-labeled protein with 13C,15N-labeled RNA.
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMPolypyrimidine-tract binding protein N-terminal RNA recognition motif[U-15N]-99%1
10 mMNaH2PO4/NaOH buffernone1
20 mMsodium chloridenone1
0.8 mMPolypyrimidine-tract binding protein N-terminal RNA recognition motif[U-13C,15N]-99%2
10 mMNaH2PO4/NaOH buffernone2
20 mMsodium chloridenone2
0.8 mMPolypyrimidine-tract binding protein N-terminal RNA recognition motif[U-15N]-99%3
10 mMNaH2PO4/NaOH buffernone3
20 mMsodium chloridenone3
0.8 mMPolypyrimidine-tract binding protein N-terminal RNA recognition motif[U-15N]-99%5
10 mMNaH2PO4/NaOH buffernone5
20 mMsodium chloridenone5
0.8 mMUCUUU-SL-RNA[U-13C,15N]-99%5
Sample conditions

Ionic strength: 33.3 mM / Ionic strength err: 0.2 / pH: 6.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature err: 0.2

Conditions-IDLabelTemperature (K)
2313K313 K
1298K298 K
3293K293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE9001Z-axis gradient triple resonance cryoprobe
Bruker AVANCEBrukerAVANCE7502Z-axis gradient triple resonance RT probe
Bruker AVANCEBrukerAVANCE7003Z-axis gradient triple resonance cryoprobe
Bruker AVANCEBrukerAVANCE5004Z-axis gradient triple resonance cryoprobe

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97betaGuntert & Buchnerstructure calculation
CYANA3.97betaGuntert & Buchnerrefinement
TopSpin3Bruker Biospinprocessing
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CYANA3.97betaWurz & Guntertpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structure was calculated using the CONSENSUS protocol of CYANA due better sample the conformational space consistent with the input data. Unlike in traditional CYANA structure ...Details: The structure was calculated using the CONSENSUS protocol of CYANA due better sample the conformational space consistent with the input data. Unlike in traditional CYANA structure calculations, in CONSENSUS structure calculations the constraint list includes ambiguous restraints. There is no refinement protocol for NMR structures using programs which have realistic energy potentials for ambiguous restraints. In addition the structure includes a highly dynamic structural element (alpha3). Therefore no standard refinement was performed.
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2000 / 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://pdbjlc1.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