[English] 日本語
Yorodumi
- PDB-2m0g: Structure, phosphorylation and U2AF65 binding of the Nterminal Do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m0g
TitleStructure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition
Components
  • Splicing factor 1
  • Splicing factor U2AF 65 kDa subunit
KeywordsSPLICING / spliceosome assembly / SF1 / UHM / ULM
Function / homology
Function and homology information


nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Leydig cell differentiation / male sex determination / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Leydig cell differentiation / male sex determination / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / spliceosomal complex assembly / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / mRNA 3'-splice site recognition / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / negative regulation of smooth muscle cell proliferation / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear body / ribosome / nuclear speck / mRNA binding / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
KH-domain type I / Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / U2 snRNP auxilliary factor, large subunit, splicing factor / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RRM (RNA recognition motif) domain / RNA recognition motif ...KH-domain type I / Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / U2 snRNP auxilliary factor, large subunit, splicing factor / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / 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 / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Splicing factor U2AF 65 kDa subunit / Splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMadl, T. / Sattler, M. / Zhang, Y. / Bagdiul, I. / Kern, T. / Kang, H. / Zou, P. / Maeusbacher, N. / Sieber, S.A. / Kraemer, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition.
Authors: Zhang, Y. / Madl, T. / Bagdiul, I. / Kern, T. / Kang, H.S. / Zou, P. / Mausbacher, N. / Sieber, S.A. / Kramer, A. / Sattler, M.
History
DepositionOct 25, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Splicing factor 1
B: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)28,6522
Polymers28,6522
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Splicing factor 1 / Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene ...Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene in MEN1 locus / Zinc finger protein 162


Mass: 16675.066 Da / Num. of mol.: 1 / Fragment: UNP residues 1-145 / Mutation: S137C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15637
#2: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 11976.615 Da / Num. of mol.: 1 / Fragment: RRM 3 domain residues 372-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Production host: Escherichia coli (E. coli) / References: UniProt: P26368

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCA
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 100-600 uM [U-15N] protein, 100-600 uM [U-13C; U-15N] entity, 100-600 uM [U-13C; U-15N; U-2H] entity, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMprotein-1[U-15N]100-6001
uMprotein-2[U-13C; U-15N]100-6001
uMprotein-3[U-13C; U-15N; U-2H]100-6001
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / 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://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