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- PDB-2m0y: Solution structure of the SH3 domain of DOCK180 -

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Basic information

Entry
Database: PDB / ID: 2m0y
TitleSolution structure of the SH3 domain of DOCK180
ComponentsDedicator of cytokinesis protein 1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


DCC mediated attractive signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Regulation of actin dynamics for phagocytic cup formation / Factors involved in megakaryocyte development and platelet production / guanyl-nucleotide exchange factor complex / VEGFA-VEGFR2 Pathway / small GTPase-mediated signal transduction / positive regulation of epithelial cell migration / hematopoietic progenitor cell differentiation / phagocytosis ...DCC mediated attractive signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Regulation of actin dynamics for phagocytic cup formation / Factors involved in megakaryocyte development and platelet production / guanyl-nucleotide exchange factor complex / VEGFA-VEGFR2 Pathway / small GTPase-mediated signal transduction / positive regulation of epithelial cell migration / hematopoietic progenitor cell differentiation / phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / GTPase activator activity / guanyl-nucleotide exchange factor activity / SH3 domain binding / cell migration / nuclear speck / apoptotic process / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
: / Dedicator of cytokinesis protein 5 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C ...: / Dedicator of cytokinesis protein 5 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / 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. / SH3 Domains / C2 domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Dedicator of cytokinesis protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLiu, X. / Wen, W.
CitationJournal: Proteins / Year: 2013
Title: Solution structure of the SH3 domain of DOCK180.
Authors: Liu, X. / Li, F. / Pan, Z. / Wang, W. / Wen, W.
History
DepositionNov 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 1


Theoretical massNumber of molelcules
Total (without water)8,6601
Polymers8,6601
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)20 / 200structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein Dedicator of cytokinesis protein 1 / 180 kDa protein downstream of CRK / DOCK180


Mass: 8659.841 Da / Num. of mol.: 1 / Fragment: SH3 domain residues 1-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dock1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BUR4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1322D 1H-15N HSQC
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D HNCO
1732D 1H-13C HSQC
1833D 1H-13C NOESY
1942D 1H-1H NOESY
11042D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N] SH3, 50 mM PBS, 1 mM DTT, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 13C; U-100% 15N] SH3, 50 mM PBS, 1 mM DTT, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-100% 13C; U-100% 15N] SH3, 50 mM PBS, 1 mM [U-100% 2H] DTT, 1 mM EDTA, 100% D2O100% D2O
40.4 mM SH3, 50 mM PBS, 1 mM [U-100% 2H] DTT, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMSH3-1[U-100% 15N]1
50 mMPBS-21
1 mMDTT-31
1 mMEDTA-41
0.4 mMSH3-5[U-100% 13C; U-100% 15N]2
50 mMPBS-62
1 mMDTT-72
1 mMEDTA-82
0.4 mMSH3-9[U-100% 13C; U-100% 15N]3
50 mMPBS-103
1 mMDTT-11[U-100% 2H]3
1 mMEDTA-123
0.4 mMSH3-134
50 mMPBS-144
1 mMDTT-15[U-100% 2H]4
1 mMEDTA-164
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardpeak picking
PIPPGarrettchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 38 / Protein psi angle constraints total count: 39
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 20

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