[English] 日本語
Yorodumi
- PDB-2rm0: FBP28WW2 domain in complex with a PPPLIPPPP peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rm0
TitleFBP28WW2 domain in complex with a PPPLIPPPP peptide
Components
  • Formin-1Formins
  • Transcription elongation regulator 1
KeywordsTRANSCRIPTION / FBP28WW2 / PPPLIPPPP ligand / Alternative splicing / Coiled coil / Nucleus / Polymorphism / Repressor / Transcription regulation / Actin-binding / Cell junction / Cytoplasm / Membrane / Phosphorylation
Function / homology
Function and homology information


ureteric bud invasion / forelimb morphogenesis / mRNA Splicing - Major Pathway / hindlimb morphogenesis / actin nucleation / positive regulation of actin nucleation / proline-rich region binding / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / skeletal system morphogenesis ...ureteric bud invasion / forelimb morphogenesis / mRNA Splicing - Major Pathway / hindlimb morphogenesis / actin nucleation / positive regulation of actin nucleation / proline-rich region binding / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / skeletal system morphogenesis / limb development / positive regulation of actin filament polymerization / positive regulation of focal adhesion assembly / RNA splicing / actin filament / transcription coregulator activity / adherens junction / mRNA processing / SH3 domain binding / transcription corepressor activity / gene expression / actin binding / microtubule binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity / DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Formin homology family, Cappuccino subfamily / Transcription elongation regulator 1-like / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / FF domain / FF domain / FF domain superfamily ...Formin homology family, Cappuccino subfamily / Transcription elongation regulator 1-like / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Formin-1 / Transcription elongation regulator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsRamirez-Espain, X. / Ruiz, L. / Martin-Malpartida, P. / Oschkinat, H. / Macias, M.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Characterization of a New Binding Motif and a Novel Binding Mode in Group 2 WW Domains
Authors: Ramirez-Espain, X. / Ruiz, L. / Martin-Malpartida, P. / Oschkinat, H. / Macias, M.J.
History
DepositionSep 6, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name
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 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
W: Transcription elongation regulator 1
P: Formin-1


Theoretical massNumber of molelcules
Total (without water)5,2892
Polymers5,2892
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area600 Å2
ΔGint-7 kcal/mol
Surface area3960 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 60structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Transcription elongation regulator 1 / / TATA box-binding protein- associated factor 2S / Transcription factor CA150 / p144 / Formin- ...TATA box-binding protein- associated factor 2S / Transcription factor CA150 / p144 / Formin- binding protein 28 / FBP 28


Mass: 4364.709 Da / Num. of mol.: 1 / Fragment: WW 2 domain, sequence database residues 430-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcerg1, Taf2s / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CGF7
#2: Protein/peptide Formin-1 / Formins / Limb deformity protein


Mass: 924.134 Da / Num. of mol.: 1 / Fragment: sequence database residues, 880-888 / Source method: obtained synthetically
Details: The authors state that the peptide was chemically synthesized and the sequence corresponds to the mouse formin protein.
Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q05860

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1233D 1H-15N NOESY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM FPB28WW2, 3 mM PPPLIPPPP, 50 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM FPB28WW2, 3 mM PPPLIPPPP, 50 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
31 mM [U-100% 15N] FPB28WW2, 3 mM PPPLIPPPP, 50 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMFPB28WW21
3 mMPPPLIPPPP1
50 mMsodium phosphate1
100 mMsodium chloride1
1 mMFPB28WW22
3 mMPPPLIPPPP2
50 mMsodium phosphate2
100 mMsodium chloride2
1 mMFPB28WW2[U-100% 15N]3
3 mMPPPLIPPPP3
50 mMsodium phosphate3
100 mMsodium chloride3
Sample conditionsIonic strength: 150 / pH: 5.8 / Pressure: ambient / Temperature: 285 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XEASYKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurstructure validation
ARIALinge, O'Donoghue and Nilgesstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure display
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 8

+
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