[English] 日本語
Yorodumi
- PDB-2btt: NMR Structure of MYO3-SH3 domain from Myosin-typeI from S. cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2btt
TitleNMR Structure of MYO3-SH3 domain from Myosin-typeI from S. cerevisiae
ComponentsMYOSIN-3 ISOFORM
KeywordsCONTRACTILE PROTEIN / SH3 DOMAIN / MYOSIN-TYPE I / MUSCLE PROTEIN / ACTIN-BINDING / ATP-BINDING / MOTOR PROTEIN / MYOSIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / cell tip / fungal-type cell wall organization / actin cortical patch / vesicle transport along actin filament / response to osmotic stress / microfilament motor activity ...bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / cell tip / fungal-type cell wall organization / actin cortical patch / vesicle transport along actin filament / response to osmotic stress / microfilament motor activity / myosin binding / exocytosis / actin filament organization / cell periphery / endocytosis / actin filament binding / actin cytoskeleton / vesicle / hydrolase activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Fungal myosin-I, SH3 domain / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains ...Fungal myosin-I, SH3 domain / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / ARIA 1.2
AuthorsMusi, V. / Birdsall, B. / Pastore, A.
CitationJournal: Protein Sci. / Year: 2006
Title: New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae.
Authors: Musi, V. / Birdsall, B. / Fernandez-Ballester, G. / Guerrini, R. / Salvatori, S. / Serrano, L. / Pastore, A.
History
DepositionJun 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.5Apr 24, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOSIN-3 ISOFORM


Theoretical massNumber of molelcules
Total (without water)7,5881
Polymers7,5881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LOWEST ENERGY
RepresentativeModel #1

-
Components

#1: Protein MYOSIN-3 ISOFORM / MYO3-SH3 DOMAIN / MYO3-SH3 ISOFORM


Mass: 7588.495 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 1122-1190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36006

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N-NOESY-HSQC
1211H-15N- TOCSY-HSQC
131HNHA
141HNHB
151CBCA(CO)NH
161CBCANH
171HNCO
181(H)CCH- TOCSY
1912D-NOESY
11012D COSY
11112D-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED MYO3_SH3.

-
Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2LINGE,HABECK,RIEPING,NILGESrefinement
XEASYstructure solution
Sparkystructure solution
RefinementMethod: ARIA 1.2 / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / 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