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- PDB-3a98: Crystal structure of the complex of the interacting regions of DO... -

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Basic information

Entry
Database: PDB / ID: 3a98
TitleCrystal structure of the complex of the interacting regions of DOCK2 and ELMO1
Components
  • Dedicator of cytokinesis protein 2
  • Engulfment and cell motility protein 1
KeywordsSIGNALING PROTEIN / protein-protein complex / DOCK2 / ELMO1 / SH3 domain / PH domain / helix bundle / proline-rich sequence / Cytoskeleton / Guanine-nucleotide releasing factor / Membrane / Phosphoprotein / Apoptosis / Cell membrane / Phagocytosis / SH3-binding
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 / small GTPase-mediated signal transduction / phagocytosis, engulfment / Rac protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / T cell receptor binding / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of phagocytosis / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / cell motility / actin filament organization / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / 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 / cytoplasm / cytosol
Similarity search - Function
Dedicator of cytokinesis N-terminal subdomain / Helicase, Ruva Protein; domain 3 - #90 / 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 ...Dedicator of cytokinesis N-terminal subdomain / Helicase, Ruva Protein; domain 3 - #90 / 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 / Helicase, Ruva Protein; domain 3 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / SH3 Domains / PH-domain like / C2 domain superfamily / Pleckstrin homology domain / Helix non-globular / Special / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHanawa-Suetsugu, K. / Kukimoto-Niino, M. / Sekine, S. / Ito, T. / Mishima-Tsumagari, C. / Terada, T. / Shirouzu, M. / Fukui, Y. / Yokoyama, S.
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: PDBJ / 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 / Derived calculations
Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 2
B: Engulfment and cell motility protein 1
C: Dedicator of cytokinesis protein 2
D: Engulfment and cell motility protein 1


Theoretical massNumber of molelcules
Total (without water)89,6224
Polymers89,6224
Non-polymers00
Water2,396133
1
A: Dedicator of cytokinesis protein 2
B: Engulfment and cell motility protein 1


Theoretical massNumber of molelcules
Total (without water)44,8112
Polymers44,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-32 kcal/mol
Surface area19990 Å2
MethodPISA
2
C: Dedicator of cytokinesis protein 2
D: Engulfment and cell motility protein 1


Theoretical massNumber of molelcules
Total (without water)44,8112
Polymers44,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-35 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.837, 104.028, 124.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dedicator of cytokinesis protein 2 / DOCK2


Mass: 21402.713 Da / Num. of mol.: 2 / Fragment: N-terminal domains, SH3 domain, residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK2, KIAA0209 / Plasmid: PX080711-01 / Production host: Cell free protein synthesis (others) / References: UniProt: Q92608
#2: Protein Engulfment and cell motility protein 1 / ELMO1 / CED-12 homolog


Mass: 23408.178 Da / Num. of mol.: 2 / Fragment: C-terminal domains, PH domain, residues 532-727
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO1, KIAA0281 / Plasmid: PX080910-01 / Production host: Cell free protein synthesis (others) / References: UniProt: Q92556
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 3350, 0.1M di-ammonium hydrogen citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97888 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97888 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49140 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 28.7
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.785 / % possible all: 100

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Processing

Software
NameVersionClassification
autoSHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1994021.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2455 5 %RANDOM
Rwork0.226 ---
obs0.226 48976 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.6634 Å2 / ksol: 0.378733 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.54 Å20 Å20 Å2
2---2.12 Å20 Å2
3----6.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 0 133 5550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 375 4.8 %
Rwork0.256 7485 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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