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- PDB-2rqr: The solution structure of human DOCK2 SH3 domain - ELMO1 peptide ... -

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Basic information

Entry
Database: PDB / ID: 2rqr
TitleThe solution structure of human DOCK2 SH3 domain - ELMO1 peptide chimera complex
ComponentsEngulfment and cell motility protein 1,Dedicator of cytokinesis protein 2
KeywordsPROTEIN BINDING / KIAA0209 / KIAA0281 / Apoptosis / Membrane / Phagocytosis / Phosphoprotein / SH3-binding / Cytoskeleton / Guanine-nucleotide releasing factor / SH3 domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / immunological synapse formation / negative thymic T cell selection / guanyl-nucleotide exchange factor complex / myoblast fusion / positive thymic T cell selection ...membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / immunological synapse formation / negative thymic T cell selection / guanyl-nucleotide exchange factor complex / myoblast fusion / positive thymic T cell selection / Nef and signal transduction / regulation of small GTPase mediated signal transduction / phagocytosis, engulfment / small GTPase-mediated signal transduction / Rac protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of phagocytosis / RAC1 GTPase cycle / T cell receptor binding / GTPase activator activity / guanyl-nucleotide exchange factor activity / actin filament organization / cell motility / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / SH3 domain binding / VEGFA-VEGFR2 Pathway / specific granule lumen / chemotaxis / cell migration / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization / cytoskeleton / apoptotic process / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dedicator of cytokinesis protein 2 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / DOCKER, Lobe A ...Dedicator of cytokinesis protein 2 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / Pleckstrin homology domain / Variant SH3 domain / SH3 Domains / C2 domain superfamily / Pleckstrin homology domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailsfewest violations, model 1
AuthorsYokoyama, S. / Tochio, N. / Koshiba, S. / Kigawa, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Authors: Hanawa-Suetsugu, K. / Kukimoto-Niino, M. / Mishima-Tsumagari, C. / Akasaka, R. / Ohsawa, N. / Sekine, S. / Ito, T. / Tochio, N. / Koshiba, S. / Kigawa, T. / Terada, T. / Shirouzu, M. / ...Authors: Hanawa-Suetsugu, K. / Kukimoto-Niino, M. / Mishima-Tsumagari, C. / Akasaka, R. / Ohsawa, N. / Sekine, S. / Ito, T. / Tochio, N. / Koshiba, S. / Kigawa, T. / Terada, T. / Shirouzu, M. / Nishikimi, A. / Uruno, T. / Katakai, T. / Kinashi, T. / Kohda, D. / Fukui, Y. / Yokoyama, S.
History
DepositionOct 21, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jan 22, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engulfment and cell motility protein 1,Dedicator of cytokinesis protein 2


Theoretical massNumber of molelcules
Total (without water)12,6361
Polymers12,6361
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Engulfment and cell motility protein 1,Dedicator of cytokinesis protein 2 / Protein ced-12 homolog


Mass: 12635.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO1, KIAA0281, DOCK2, KIAA0209 / Plasmid: P070313-06 / Production host: Cell-free synthesis (others) / References: UniProt: Q92556, UniProt: Q92608

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] protein, 20mM [U-2H] TRIS-2, 100mM sodium chloride-3, 0.02% sodium azide-4, 1mM [U-2H] DTT-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C; U-100% 15N]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
0.02 %sodium azide-41
1 mMDTT-5[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAKobayashidata analysis
CYANAGuntert, Mumenthaler, Wuthrichstructure solution
CYANAGuntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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