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- PDB-3vhl: Crystal structure of the DHR-2 domain of DOCK8 in complex with Cd... -

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Basic information

Entry
Database: PDB / ID: 3vhl
TitleCrystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
Components
  • Cell division control protein 42 homolog
  • Dedicator of cytokinesis protein 8
KeywordsSIGNALING PROTEIN / signal transduction / guanine nucleotide exchang factor / GTPase
Function / homology
Function and homology information


memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure ...memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / immunological synapse formation / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / Factors involved in megakaryocyte development and platelet production / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / negative regulation of T cell apoptotic process / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / cell leading edge / RHO GTPases activate PAKs / lamellipodium membrane / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / positive regulation of T cell migration / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of establishment of T cell polarity / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / filopodium / positive regulation of DNA replication / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis
Similarity search - Function
Dedicator of cytokinesis C, C2 domain / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B / Dedicator of cytokinesis ...Dedicator of cytokinesis C, C2 domain / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / 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. / Cdc42 / 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 / 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
PHOSPHATE ION / Cell division control protein 42 homolog / Dedicator of cytokinesis protein 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.085 Å
AuthorsHanawa-Suetsugu, K. / Kukimoto-Niino, M. / Nishizak, T. / Terada, T. / Shirouzu, M. / Fukui, Y. / Yokoyama, S.
CitationJournal: Blood / Year: 2012
Title: DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses.
Authors: Harada, Y. / Tanaka, Y. / Terasawa, M. / Pieczyk, M. / Habiro, K. / Katakai, T. / Hanawa-Suetsugu, K. / Kukimoto-Niino, M. / Nishizaki, T. / Shirouzu, M. / Duan, X. / Uruno, T. / Nishikimi, ...Authors: Harada, Y. / Tanaka, Y. / Terasawa, M. / Pieczyk, M. / Habiro, K. / Katakai, T. / Hanawa-Suetsugu, K. / Kukimoto-Niino, M. / Nishizaki, T. / Shirouzu, M. / Duan, X. / Uruno, T. / Nishikimi, A. / Sanematsu, F. / Yokoyama, S. / Stein, J.V. / Kinashi, T. / Fukui, Y.
History
DepositionAug 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 8
B: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4524
Polymers55,2622
Non-polymers1902
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-37 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.185, 73.279, 65.031
Angle α, β, γ (deg.)90.00, 104.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-208-

HOH

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Components

#1: Protein Dedicator of cytokinesis protein 8


Mass: 33787.785 Da / Num. of mol.: 1 / Fragment: DHR-2 domain (UNP RESIDUES 1787-2067)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dock8 / Plasmid: PX101019-11 / Production host: cell-free protein synthsis (unknown) / References: UniProt: Q8C147
#2: Protein Cell division control protein 42 homolog / Cdc42 / G25K GTP-binding protein


Mass: 21474.535 Da / Num. of mol.: 1 / Mutation: T17N, C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: PX080214-12 / Production host: cell-free protein synthsis (unknown) / References: UniProt: P60953
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Potassium phosphate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.085→30 Å / Num. obs: 28080 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.06 / Net I/σ(I): 24.6
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.96 / Rsym value: 0.338 / % possible all: 98.4

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Processing

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

2wm9


Resolution: 2.085→29.679 Å / SU ML: 0.55 / σ(F): 0 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1905 7.18 %RANDOM
Rwork0.1785 ---
obs0.1823 26517 93.68 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.677 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3048 Å20 Å27.3091 Å2
2--0.2683 Å20 Å2
3---3.0365 Å2
Refinement stepCycle: LAST / Resolution: 2.085→29.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 10 194 3781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013665
X-RAY DIFFRACTIONf_angle_d1.2754956
X-RAY DIFFRACTIONf_dihedral_angle_d15.2171396
X-RAY DIFFRACTIONf_chiral_restr0.1547
X-RAY DIFFRACTIONf_plane_restr0.007639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0848-2.1370.28251240.1916161687
2.137-2.19470.27381370.1898173493
2.1947-2.25930.26151340.1787175394
2.2593-2.33220.27991340.1829172391
2.3322-2.41550.27121280.1922164490
2.4155-2.51220.27451340.1863173292
2.5122-2.62640.25831310.1987171291
2.6264-2.76480.29841350.2116169790
2.7648-2.93790.32861310.2093169491
2.9379-3.16450.20341400.1982178996
3.1645-3.48250.22161450.17411880100
3.4825-3.98540.19911430.1615185398
3.9854-5.01730.17651420.1408186299
5.0173-29.68190.22981470.1875192399
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)
12.7318-0.4729-0.47284.78580.23522.32790.07580.04840.0565-0.1830.0251-0.1409-0.0954-0.1104-0.06140.1447-0.0359-0.01090.12920.01910.148636.8503-5.9088-6.5282
21.0328-0.0803-0.20570.85110.24370.4403-0.0642-0.02860.0513-0.07180.1143-0.014-0.0341-0.0386-0.06750.20160.0125-0.00790.16880.03070.239634.39478.62372.9862
34.22330.7413-2.02433.0637-1.53943.83150.1569-0.3810.28160.4036-0.0476-0.1335-0.5247-0.0412-0.1640.24340.0943-0.06520.2248-0.09780.202433.020120.368720.6824
49.1222-6.19673.91834.2778-2.85117.58810.59980.77840.0929-0.3179-0.42370.38080.1239-0.4716-0.19120.1578-0.04470.00390.34220.04620.235522.4624-2.057420.6439
50.5744-0.46570.00322.7423-0.41342.33480.0851-0.01670.0775-0.1225-0.1341-0.04530.2532-0.14750.07820.19940.00430.02980.25620.0290.19431.4265-1.184312.7408
62.4790.48012.33718.63010.452.5588-0.057-0.26440.25410.6003-0.011-0.8445-0.50891.48990.22790.3745-0.0239-0.06140.46530.06650.346837.04871.689132.9837
71.9211-0.5819-0.14791.7710.07222.3409-0.0822-0.0052-0.24360.09360.10440.0050.3753-0.25350.00730.2599-0.07190.00310.22620.01780.188135.2816-14.324524.0574
85.9105-4.7762-1.00995.35992.18086.10820.13560.1933-0.5764-0.241-0.12150.22120.3288-0.5042-0.00570.2263-0.0818-0.06440.22930.02140.219722.6433-11.06714.9478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1792:1890)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1891:1980)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 1981:2062)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 1:10)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 11:57)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 58:67)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 68:164)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 165:178)

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