[English] 日本語
Yorodumi
- PDB-2a36: Solution structure of the N-terminal SH3 domain of DRK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a36
TitleSolution structure of the N-terminal SH3 domain of DRK
ComponentsProtein E(sev)2B
KeywordsSIGNALING PROTEIN / DROSOPHILA MELANOGASTER / SH3 FRAGMENT / DRK
Function / homology
Function and homology information


PI3K Cascade / Generation of second messenger molecules / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SOS-mediated signalling / Signaling by SCF-KIT ...PI3K Cascade / Generation of second messenger molecules / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SOS-mediated signalling / Signaling by SCF-KIT / Regulation of KIT signaling / Signalling to RAS / Downstream signal transduction / DAP12 signaling / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / Signal attenuation / Insulin receptor signalling cascade / RET signaling / FLT3 Signaling / FCERI mediated MAPK activation / PIP3 activates AKT signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sevenless binding / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / torso signaling pathway / NCAM signaling for neurite out-growth / tracheal outgrowth, open tracheal system / Spry regulation of FGF signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of signaling by CBL / RAF/MAP kinase cascade / EGFR downregulation / RHOU GTPase cycle / Cargo recognition for clathrin-mediated endocytosis / RHO GTPases Activate WASPs and WAVEs / epithelial cell migration, open tracheal system / Regulation of actin dynamics for phagocytic cup formation / R7 cell fate commitment / sevenless signaling pathway / follicle cell of egg chamber development / Clathrin-mediated endocytosis / imaginal disc-derived wing morphogenesis / short-term memory / olfactory learning / COP9 signalosome / epidermal growth factor receptor binding / associative learning / regulation of MAPK cascade / fibroblast growth factor receptor signaling pathway / positive regulation of cell size / vascular endothelial growth factor receptor signaling pathway / phosphotyrosine residue binding / positive regulation of TORC1 signaling / sensory perception of sound / positive regulation of receptor-mediated endocytosis / epidermal growth factor receptor signaling pathway / insulin receptor signaling pathway / signaling receptor complex adaptor activity / presynapse / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / signal transduction / protein-containing complex / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. ...Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsForman-Kay, J.D. / Bezsonova, I. / Singer, A. / Choy, W.-Y. / Tollinger, M.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Comparison of the Unstable drkN SH3 Domain and a Stable Mutant
Authors: Bezsonova, I. / Singer, A. / Choy, W.-Y. / Tollinger, M. / Forman-Kay, J.D.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 400COMPOUND RESIDUE ANI PRESENT IN THE CONSTRAINT FILE DEFINES THE ALIGNMENT FRAME. INCLUDE THESE ...COMPOUND RESIDUE ANI PRESENT IN THE CONSTRAINT FILE DEFINES THE ALIGNMENT FRAME. INCLUDE THESE COORDINATES TO USE THE RESIDUAL DIPOLAR COUPLING AND/OR CARBONYL CHEMICAL SHIFT RESTRAINTS

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein E(sev)2B


Theoretical massNumber of molelcules
Total (without water)6,8691
Polymers6,8691
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 Protein E(sev)2B / Protein enhancer of sevenless 2B / SH2-SH3 adapter protein drk / Downstream of receptor kinase


Mass: 6868.628 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN, RESIDUES 1-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: drk, E(sev)2B / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q08012

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 200 ms NOESY
1213D 150 ms 15N-edited NOESY
1312D 150 ms NOESY
1411H/D amide exchange experiment
151HNCO-based 3D experiments
NMR detailsText: HNCO-based 3D experiments were used for measuring 15N-1HN, 15N-13C', 13C'-13CA RDCs and C'-CSA restraints.13CA-13CB and 13CA-1HA RDCs were also measured.

-
Sample preparation

DetailsContents: 1MM DRKN SH3 DOMAIN 15N,13C, 500 MM NA2SO4, 50 MM PHOSPHATE BUFFER, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 500mM / pH: 6 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGERstructure solution
CNS1BRUNGERrefinement
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