[English] 日本語
Yorodumi
- PDB-2km8: Interdomain RRM packing contributes to RNA recognition in the rna... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2km8
TitleInterdomain RRM packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3' processing ternary complex
Components
  • 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
  • Nuclear polyadenylated RNA-binding protein 4
  • mRNA 3'-end-processing protein RNA15
KeywordsRNA binding protein/RNA / 3' processing / RRM domain / rna15p / hrp1p / enhancer element / positioning element / RNA recognition / mRNA processing / Nucleus / RNA-binding / Nonsense-mediated mRNA decay / Phosphoprotein / RNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


mRNA cleavage stimulating factor complex / response to DNA damage checkpoint signaling / mRNA cleavage factor complex / mRNA cleavage and polyadenylation specificity factor complex / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA processing / cytoplasmic stress granule / regulation of translation / molecular adaptor activity ...mRNA cleavage stimulating factor complex / response to DNA damage checkpoint signaling / mRNA cleavage factor complex / mRNA cleavage and polyadenylation specificity factor complex / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA processing / cytoplasmic stress granule / regulation of translation / molecular adaptor activity / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
HRP1, RNA recognition motif 1 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / 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 ...HRP1, RNA recognition motif 1 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / 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 / RNA (> 10) / mRNA 3'-end-processing protein RNA15 / Nuclear polyadenylated RNA-binding protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLeeper, T.C. / Varani, G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1.
Authors: Leeper, T.C. / Qu, X. / Lu, C. / Moore, C. / Varani, G.
History
DepositionJul 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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: 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
B: mRNA 3'-end-processing protein RNA15
C: Nuclear polyadenylated RNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)32,5133
Polymers32,5133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'


Mass: 4096.478 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein mRNA 3'-end-processing protein RNA15 / rna15p


Mass: 9350.483 Da / Num. of mol.: 1 / Fragment: UNP residues 14 to 97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: 2.1, RNA15, YGL044C / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys / References: UniProt: P25299
#3: Protein Nuclear polyadenylated RNA-binding protein 4 / Cleavage factor IB / CFIB / hrp1p


Mass: 19065.559 Da / Num. of mol.: 1 / Fragment: UNP residues 156 to 322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRP1, NAB4, NAB5, YOL123W / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys / References: UniProt: Q99383

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of rna15p and hrp1p proteins bound to RNA refined with PREs and RDCs.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
1532D 1H-13C HSQC
1642D 1H-13C HSQC
1752D 1H-13C HSQC
1853D HNCO
1953D HNCA
11053D HN(CA)CB
11153D HN(CO)CA
11253D CBCA(CO)NH
11353D (H)CCH-TOCSY
11453D 1H-15N TOCSY
11553D 1H-15N NOESY
11653D 1H-13C NOESY
11763D 1H-15N NOESY
11863D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N] rna15p-1, 0.4 mM hrp1p-2, 0.4 mM anchor RNA-3, 93% H2O/7% D2O93% H2O/7% D2O
20.6 mM rna15p-4, 0.6 mM [U-100% 15N] hrp1p-5, 0.6 mM anchor RNA-6, 93% H2O/7% D2O93% H2O/7% D2O
30.35 mM [U-100% 13C] rna15p-7, 0.35 mM [U-100% 15N] hrp1p-8, 0.35 mM anchor RNA-9, 93% H2O/7% D2O93% H2O/7% D2O
40.5 mM [U-100% 15N] rna15p-10, 0.5 mM [U-100% 13C] hrp1p-11, 0.5 mM anchor RNA-12, 93% H2O/7% D2O93% H2O/7% D2O
50.5 mM [U-100% 13C; U-100% 15N] rna15p-13, 0.5 mM hrp1p-14, 0.5 mM anchor RNA-15, 93% H2O/7% D2O93% H2O/7% D2O
60.5 mM rna15p-16, 0.5 mM [U-100% 13C; U-100% 15N] hrp1p-17, 0.5 mM anchor RNA-18, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMrna15p-1[U-100% 15N]1
0.4 mMhrp1p-21
0.4 mManchor RNA-31
0.6 mMrna15p-42
0.6 mMhrp1p-5[U-100% 15N]2
0.6 mManchor RNA-62
0.35 mMrna15p-7[U-100% 13C]3
0.35 mMhrp1p-8[U-100% 15N]3
0.35 mManchor RNA-93
0.5 mMrna15p-10[U-100% 15N]4
0.5 mMhrp1p-11[U-100% 13C]4
0.5 mManchor RNA-124
0.5 mMrna15p-13[U-100% 13C; U-100% 15N]5
0.5 mMhrp1p-145
0.5 mManchor RNA-155
0.5 mMrna15p-166
0.5 mMhrp1p-17[U-100% 13C; U-100% 15N]6
0.5 mManchor RNA-186
Sample conditionsIonic strength: 160 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
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: 10

+
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://pdbjlvh1.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