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- PDB-7clx: Crystal structure of the DOCK8 DHR-1 domain -

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Basic information

Entry
Database: PDB / ID: 7clx
TitleCrystal structure of the DOCK8 DHR-1 domain
ComponentsDedicator of cytokinesis protein 8
KeywordsSIGNALING PROTEIN / Guanine nucleotide exchange factor / Dock / Rho GTPase / Cdc42 / membrane / phosphoinositide
Function / homology
Function and homology information


memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / dendritic cell migration / immunological synapse formation / Factors involved in megakaryocyte development and platelet production / leading edge membrane / negative regulation of T cell apoptotic process / cellular response to chemokine ...memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / dendritic cell migration / immunological synapse formation / Factors involved in megakaryocyte development and platelet production / leading edge membrane / negative regulation of T cell apoptotic process / cellular response to chemokine / small GTPase-mediated signal transduction / cell leading edge / lamellipodium membrane / positive regulation of T cell migration / positive regulation of establishment of T cell polarity / guanyl-nucleotide exchange factor activity / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dedicator of cytokinesis C, C2 domain / 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 ...Dedicator of cytokinesis C, C2 domain / 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. / C2 domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Dedicator of cytokinesis protein 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKukimoto-Niino, M. / Shirouzu, M. / Yokoyama, S. / Fukui, Y. / Uruno, T.
CitationJournal: Life Sci Alliance / Year: 2021
Title: A conserved PI(4,5)P2-binding domain is critical for immune regulatory function of DOCK8.
Authors: Sakurai, T. / Kukimoto-Niino, M. / Kunimura, K. / Yamane, N. / Sakata, D. / Aihara, R. / Yasuda, T. / Yokoyama, S. / Shirouzu, M. / Fukui, Y. / Uruno, T.
History
DepositionJul 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)21,4821
Polymers21,4821
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.275, 89.275, 49.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-890-

HOH

21A-904-

HOH

31A-1030-

HOH

41A-1031-

HOH

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Components

#1: Protein Dedicator of cytokinesis protein 8


Mass: 21482.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dock8 / Production host: Escherichia coli (E. coli) / Strain (production host): Cell-free protein synthesis / References: UniProt: Q8C147
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, di-sodium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 32687 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rrim(I) all: 0.073 / Net I/σ(I): 35.8
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 3182 / Rrim(I) all: 0.886 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→33.146 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.08
RfactorNum. reflection% reflection
Rfree0.1986 1668 5.11 %
Rwork0.1753 --
obs0.1764 32634 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→33.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 234 1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051481
X-RAY DIFFRACTIONf_angle_d0.8482015
X-RAY DIFFRACTIONf_dihedral_angle_d15.691543
X-RAY DIFFRACTIONf_chiral_restr0.082221
X-RAY DIFFRACTIONf_plane_restr0.005257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.498-1.54210.28531420.2572485X-RAY DIFFRACTION98
1.5421-1.59190.27231350.22692528X-RAY DIFFRACTION100
1.5919-1.64880.23591360.21732544X-RAY DIFFRACTION100
1.6488-1.71480.21811210.19612560X-RAY DIFFRACTION100
1.7148-1.79280.21311380.19692533X-RAY DIFFRACTION100
1.7928-1.88730.21561390.18192579X-RAY DIFFRACTION100
1.8873-2.00560.19291520.16142546X-RAY DIFFRACTION100
2.0056-2.16040.19011390.16772570X-RAY DIFFRACTION100
2.1604-2.37780.19331570.17042575X-RAY DIFFRACTION100
2.3778-2.72170.23361360.18492610X-RAY DIFFRACTION100
2.7217-3.42850.18561350.16582649X-RAY DIFFRACTION100
3.4285-33.15380.16971380.16172787X-RAY DIFFRACTION100
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)
11.12020.5468-1.23832.0241-0.5572.12080.0963-0.16350.04240.0682-0.155-0.1218-0.17020.22960.01230.1664-0.0104-0.00130.15160.02940.1927-15.93116.8458-2.9144
24.25351.2174-3.19282.3739-0.09024.35240.0182-0.73510.05460.3502-0.17030.43020.16030.00880.0740.188-0.02810.04410.1774-0.01160.2038-28.9737-8.69232.2263
35.48391.32172.58136.35142.48047.43830.1701-0.04850.08640.3089-0.0051-0.26770.2510.0358-0.17080.10750.00130.00490.10830.02770.1208-10.8144-5.8388-4.4261
41.6582-2.1102-1.24423.0070.39491.5491-0.1591-0.25940.11330.37880.2101-0.0288-0.12560.0266-0.03210.18460.0339-0.00060.173-0.02330.1508-20.39850.20446.4312
52.65630.9756-0.02182.6049-0.41483.10150.0164-0.0341-0.0639-0.08170.07320.07760.1124-0.0692-0.04760.07730.01330.00180.07790.02520.1122-17.507-4.641-7.4005
64.46773.1472-1.59718.73650.71054.97070.08451.36760.71750.67740.85631.2326-0.3224-0.404-0.80281.24480.01750.35890.87560.18250.9497-30.6793-25.137910.8055
73.35730.3355-0.44824.9781-2.69956.33460.0021-0.2211-0.29840.18270.0670.01220.3788-0.1302-0.02880.1692-0.0292-0.01490.13990.02550.1654-25.0625-12.0711-4.9807
84.3080.9835-1.11262.26170.04721.8984-0.07140.84640.3791-0.39410.16350.2828-0.1341-0.3172-0.22740.205-0.0133-0.02820.26960.09510.2385-24.70312.1469-15.3639
94.89812.3235-1.42732.19550.92273.6592-0.23750.6488-0.3099-0.25460.115-0.01750.206-0.28750.07970.1917-0.0321-0.00450.2336-0.00990.1934-28.052-14.4725-14.8135
101.2172-0.3714-1.34220.64630.11341.41570.208-0.13330.55240.1175-0.13420.2732-0.11190.0853-0.06980.13580.0071-0.02150.16360.03860.16-23.51672.7209-5.1148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 557 through 571 )
2X-RAY DIFFRACTION2chain 'A' and (resid 572 through 590 )
3X-RAY DIFFRACTION3chain 'A' and (resid 591 through 607 )
4X-RAY DIFFRACTION4chain 'A' and (resid 608 through 631 )
5X-RAY DIFFRACTION5chain 'A' and (resid 632 through 653 )
6X-RAY DIFFRACTION6chain 'A' and (resid 654 through 663 )
7X-RAY DIFFRACTION7chain 'A' and (resid 664 through 673 )
8X-RAY DIFFRACTION8chain 'A' and (resid 674 through 687 )
9X-RAY DIFFRACTION9chain 'A' and (resid 688 through 715 )
10X-RAY DIFFRACTION10chain 'A' and (resid 716 through 736 )

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