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- PDB-3b13: Crystal structure of the DHR-2 domain of DOCK2 in complex with Ra... -

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Basic information

Entry
Database: PDB / ID: 3b13
TitleCrystal structure of the DHR-2 domain of DOCK2 in complex with Rac1 (T17N mutant)
Components
  • Dedicator of cytokinesis protein 2
  • Ras-related C3 botulinum toxin substrate 1
KeywordsPROTEIN BINDING/SIGNALING PROTEIN / protein-ptotein complex / lymphocyte chemotaxis / signal tansduction / guanine nucleotide exchange factor / GTPase / PROTEIN BINDING-SIGNALING PROTEIN complex
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 / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 ...membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / immunological synapse formation / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / negative thymic T cell selection / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / myoblast fusion / positive thymic T cell selection / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of phagocytosis / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / T cell receptor binding / GTPase activator activity / cell chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility
Similarity search - Function
DOCK DHR2 domain, lobe A / Dedicator of cytokinesis protein 2 / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C ...DOCK DHR2 domain, lobe A / Dedicator of cytokinesis protein 2 / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / 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. / Variant SH3 domain / Small GTPase Rho / small GTPase Rho family profile. / C2 domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Dedicator of cytokinesis protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.006 Å
AuthorsHanawa-Suetsugu, K. / Kukimoto-Niino, M. / 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
DepositionJun 24, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 2
B: Ras-related C3 botulinum toxin substrate 1
C: Dedicator of cytokinesis protein 2
D: Ras-related C3 botulinum toxin substrate 1


Theoretical massNumber of molelcules
Total (without water)142,6974
Polymers142,6974
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-66 kcal/mol
Surface area55480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.651, 168.651, 129.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Dedicator of cytokinesis protein 2


Mass: 51105.141 Da / Num. of mol.: 2 / Fragment: DHR-2 domain (UNP RESIDUES 1196-1622)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK2, KIAA0209 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92608
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20243.232 Da / Num. of mol.: 2 / Fragment: GTPase domain (UNP RESIDUES 1-177) / Mutation: T17N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Plasmid: PX080214-11 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P63000
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM sodium citrate, 15% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 41625 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.21 % / Rsym value: 0.129 / Net I/σ(I): 9.08
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 1.94 / Rsym value: 0.594 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WM9, 2NZ8

2wm9

2nz8


Resolution: 3.006→48.685 Å / SU ML: 0.86 / σ(F): 1.35 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 2091 5.03 %RANDOM
Rwork0.1826 ---
obs0.1853 41565 99.58 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.71 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8611 Å20 Å2-0 Å2
2--2.8611 Å2-0 Å2
3----5.7223 Å2
Refinement stepCycle: LAST / Resolution: 3.006→48.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9898 0 0 10 9908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910140
X-RAY DIFFRACTIONf_angle_d1.23913724
X-RAY DIFFRACTIONf_dihedral_angle_d15.6913842
X-RAY DIFFRACTIONf_chiral_restr0.0941468
X-RAY DIFFRACTIONf_plane_restr0.0061776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0063-3.07630.37231430.3332261699
3.0763-3.15320.35541300.28652598100
3.1532-3.23840.34911270.25652655100
3.2384-3.33370.32561370.22782635100
3.3337-3.44130.29781420.2092651100
3.4413-3.56420.22961360.19162602100
3.5642-3.70690.24871390.19382622100
3.7069-3.87550.23091520.17932628100
3.8755-4.07980.21261490.15082649100
4.0798-4.33520.181360.13322649100
4.3352-4.66970.18911320.12862619100
4.6697-5.13920.18321480.13772649100
5.1392-5.88170.22971280.1754265399
5.8817-7.40620.20691540.1814262599
7.4062-48.69170.19761380.1782262397
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4013-0.46880.76420.6821-0.26662.46590.0074-0.0477-0.09630.07380.0517-0.0201-0.04570.2155-0.05260.11510.0937-0.0140.2151-0.00390.1865-27.7098-56.572515.7428
22.0519-0.7974-1.06010.71370.04861.33790.12160.01770.33480.17230.0344-0.0948-0.3256-0.0647-0.08280.34160.10590.0460.0910.01410.1289-45.6199-41.451140.3673
32.78030.282-0.79471.6652-0.84691.1799-0.00240.1987-0.10.2708-0.0966-0.05350.14410.32270.09310.18480.05380.07980.1921-0.00640.2113-45.0674-56.229845.0807
46.72730.3685-2.37331.6805-0.77198.5583-0.30350.4701-0.4213-0.00460.1659-0.21920.80560.32460.14140.13990.07120.02710.15920.02130.2877-49.5708-60.028438.4161
52.936-1.1590.68921.7919-0.50162.8292-0.1016-0.1409-0.21260.4440.04310.45270.2986-0.36230.02840.31650.00930.15970.15440.00590.2888-57.6785-63.913952.6156
63.00841.7217-3.37080.9886-1.81848.3403-0.103-0.6829-0.23030.51690.1053-0.5178-0.12480.7963-0.02650.55680.2207-0.02830.3417-0.01020.3048-36.1757-65.948264.9794
70.605-0.0450.06370.7827-0.82121.8017-0.1524-0.0874-0.3299-0.10520.09350.05790.72120.09220.00280.44890.08680.08190.13890.04680.2623-45.6772-70.995250.8124
80.5317-0.44620.33761.2912-0.67392.2081-0.0939-0.00780.08710.08160.06890.0742-0.3763-0.1407-0.0040.26170.2636-0.12760.1058-0.00030.2035-55.3959-29.822-16.4761
91.3597-0.8985-0.14542.04341.33841.7340.00430.11910.13390.06670.0942-0.2772-0.11010.258-0.04520.09210.0961-0.01450.23720.01520.1242-39.5473-48.2578-40.55
102.90110.1522-0.19714.19050.17211.2791-0.00470.1438-0.18940.2617-0.1034-0.4338-0.2779-0.07020.07030.16560.1014-0.01910.1458-0.00120.2193-58.1018-50.8285-44.6686
111.5305-2.4846-0.37914.60440.5390.10450.02570.3202-0.1762-0.0381-0.2270.1906-0.3659-0.24740.12590.40220.019-0.03180.2424-0.10790.2152-50.7445-41.5644-44.6641
122.3636-0.5571.3013.68550.88352.4387-0.1246-0.24750.10210.236-0.0317-0.04890.0507-0.12540.13690.19620.14640.00190.1826-0.01210.2698-58.8528-51.7283-38.0799
135.80090.4886-0.51337.522-3.5056.17060.21060.7233-0.5006-1.0152-0.1397-0.48740.50930.62990.02770.22770.10860.02310.2758-0.12930.2948-51.8186-64.5982-53.6757
142.2685-0.7326-0.63652.0892-0.212.28230.03380.2949-0.41980.0116-0.01370.35850.0029-0.2562-0.00330.15240.0905-0.02020.2608-0.11160.2639-64.6557-58.7444-51.9284
152.5443-0.08960.37171.94871.85053.78510.1560.7620.5339-0.5921-0.05070.2395-1.1213-0.3088-0.06590.4770.19240.01920.40060.09650.3076-65.0095-38.357-64.4881
161.6398-0.4399-0.3590.67010.00180.51120.10360.369-0.0163-0.0478-0.01770.2707-0.1874-0.3185-0.21480.20990.17430.00870.39-0.01660.3461-72.8146-50.4139-60.3089
172.99262.0628-0.42012.6284-0.22030.39950.14220.0150.4085-0.06-0.08970.3075-0.1615-0.07110.00230.21260.14510.09320.304-0.00720.2662-67.8484-44.6659-48.8375
181.3779-0.49580.12444.5964-1.14364.1650.0069-0.264-0.31830.34510.11880.6952-0.2711-0.6194-0.13620.11920.03020.04470.30.01240.2022-67.7843-49.3983-39.0754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 1196:1436)
2X-RAY DIFFRACTION2chain A and (resseq 1437:1622)
3X-RAY DIFFRACTION3chain B and (resseq 1:39)
4X-RAY DIFFRACTION4chain B and (resseq 40:61)
5X-RAY DIFFRACTION5chain B and (resseq 62:115)
6X-RAY DIFFRACTION6chain B and (resseq 116:131)
7X-RAY DIFFRACTION7chain B and (resseq 132:177)
8X-RAY DIFFRACTION8chain C and (resseq 1196:1449)
9X-RAY DIFFRACTION9chain C and (resseq 1450:1622)
10X-RAY DIFFRACTION10chain D and (resseq 1:24)
11X-RAY DIFFRACTION11chain D and (resseq 25:39)
12X-RAY DIFFRACTION12chain D and (resseq 40:61)
13X-RAY DIFFRACTION13chain D and (resseq 62:71)
14X-RAY DIFFRACTION14chain D and (resseq 72:115)
15X-RAY DIFFRACTION15chain D and (resseq 116:131)
16X-RAY DIFFRACTION16chain D and (resseq 132:149)
17X-RAY DIFFRACTION17chain D and (resseq 150:164)
18X-RAY DIFFRACTION18chain D and (resseq 165:177)

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