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- PDB-7cly: Structure of the DOCK8 DHR-1 domain crystallized with di-C8-phosp... -

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Basic information

Entry
Database: PDB / ID: 7cly
TitleStructure of the DOCK8 DHR-1 domain crystallized with di-C8-phosphatidylinositol-(4,5)-bisphosphate
ComponentsDedicator of cytokinesis protein 8
KeywordsSIGNALING PROTEIN / Dock / guanine nucleotide exchange factor / GTPase / Cdc42 / membrane / di-C8-PI(4 / 5)P2 / 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 / cellular response to chemokine / Factors involved in megakaryocyte development and platelet production / leading edge membrane / negative regulation of T cell apoptotic process ...memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / dendritic cell migration / immunological synapse formation / cellular response to chemokine / Factors involved in megakaryocyte development and platelet production / leading edge membrane / negative regulation of T cell apoptotic process / 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 / positive regulation of GTPase activity / cytoplasm
Similarity search - Function
Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Dedicator of cytokinesis / 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 / C2 DOCK-type domain profile. ...Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Dedicator of cytokinesis / 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 / C2 DOCK-type domain profile. / DOCKER domain profile. / DOCKER domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.432 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water3,675204
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)89.046, 89.046, 49.437
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-859-

HOH

21A-896-

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.: 204 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 3350, sodium sulfate decahydrate

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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: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 37170 / % possible obs: 99.8 % / Redundancy: 12.9 % / Rrim(I) all: 0.07 / Net I/σ(I): 37
Reflection shellResolution: 1.43→1.48 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3588 / Rrim(I) all: 0.963 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLX
Resolution: 1.432→33.084 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1856 5.01 %
Rwork0.1946 --
obs0.1957 37082 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.432→33.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 0 204 1634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051472
X-RAY DIFFRACTIONf_angle_d0.8192003
X-RAY DIFFRACTIONf_dihedral_angle_d17.379539
X-RAY DIFFRACTIONf_chiral_restr0.082220
X-RAY DIFFRACTIONf_plane_restr0.005255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.432-1.47070.28551320.26842650X-RAY DIFFRACTION100
1.4707-1.5140.28591450.24422667X-RAY DIFFRACTION100
1.514-1.56290.26331210.23492696X-RAY DIFFRACTION100
1.5629-1.61870.22661330.2222680X-RAY DIFFRACTION100
1.6187-1.68360.21661460.2132668X-RAY DIFFRACTION100
1.6836-1.76020.24411270.20852698X-RAY DIFFRACTION100
1.7602-1.8530.21711500.19942691X-RAY DIFFRACTION100
1.853-1.9690.21591600.19142658X-RAY DIFFRACTION100
1.969-2.1210.21251450.1842717X-RAY DIFFRACTION100
2.121-2.33440.17471640.18112691X-RAY DIFFRACTION100
2.3344-2.67210.26491430.19342736X-RAY DIFFRACTION100
2.6721-3.36610.21521480.18482774X-RAY DIFFRACTION100
3.3661-33.09260.20321420.19162900X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.57110.7356-0.09442.24190.29531.84690.1199-0.2524-0.25680.1234-0.065-0.07850.01930.0386-0.03970.1219-0.00550.00450.1059-0.00290.0819.35992.8351-1.3364
21.9944-1.5142-0.75442.7959-0.76352.7757-0.196-0.38440.16620.4410.2079-0.2848-0.17490.2102-0.05390.14310.022-0.03040.153-0.03440.154820.83965.74991.8572
33.92911.42270.87433.7047-0.0361.838-0.05720.42780.0018-0.27470.0307-0.0839-0.13750.14740.02970.1343-0.00570.04770.1785-0.03720.132126.22045.9932-11.176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 557 through 607 )
2X-RAY DIFFRACTION2chain 'A' and (resid 608 through 664 )
3X-RAY DIFFRACTION3chain 'A' and (resid 665 through 735 )

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