|Entry||Database: PDB / ID: 3vhl|
|Title||Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)|
|Keywords||SIGNALING PROTEIN / signal transduction / guanine nucleotide exchang factor / GTPase|
|Function / homology|
Function and homology information
memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / GBD domain binding / endothelin receptor signaling pathway involved in heart process / positive regulation of pinocytosis / Golgi transport complex / modification of synaptic structure / cardiac neural crest cell migration involved in outflow tract morphogenesis ...memory T cell proliferation / RHOJ GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / GBD domain binding / endothelin receptor signaling pathway involved in heart process / positive regulation of pinocytosis / Golgi transport complex / modification of synaptic structure / cardiac neural crest cell migration involved in outflow tract morphogenesis / Cdc42 protein signal transduction / organelle transport along microtubule / dendritic cell migration / modulation by host of viral process / storage vacuole / immunological synapse formation / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of pseudopodium assembly / regulation of attachment of spindle microtubules to kinetochore / cardiac conduction system development / cell junction assembly / Inactivation of CDC42 and RAC1 / GTP-dependent protein binding / cellular response to chemokine / Factors involved in megakaryocyte development and platelet production / establishment of epithelial cell apical/basal polarity / leading edge membrane / regulation of filopodium assembly / establishment of Golgi localization / neuropilin signaling pathway / RHO GTPases activate KTN1 / negative regulation of T cell apoptotic process / embryonic heart tube development / filopodium assembly / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of stress fiber assembly / dendritic spine morphogenesis / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / RHOV GTPase cycle / regulation of mitotic nuclear division / heart contraction / regulation of protein binding / positive regulation of cytokinesis / positive regulation of phosphatidylinositol 3-kinase activity / RHOJ GTPase cycle / Golgi organization / small GTPase mediated signal transduction / RHOQ GTPase cycle / establishment or maintenance of cell polarity / cell leading edge / RHO GTPases activate PAKs / Myogenesis / positive regulation of actin cytoskeleton reorganization / macrophage differentiation / CDC42 GTPase cycle / RHOU GTPase cycle / RHOG GTPase cycle / lamellipodium membrane / RHO GTPases activate IQGAPs / positive regulation of T cell migration / negative regulation of protein-containing complex assembly / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases Activate WASPs and WAVEs / G beta:gamma signalling through CDC42 / substantia nigra development / phagocytic vesicle / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / G protein activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of establishment of T cell polarity / RAC1 GTPase cycle / small monomeric GTPase / guanyl-nucleotide exchange factor activity / actin filament organization / phagocytosis, engulfment / filopodium / cellular response to type II interferon / RHO GTPases Activate Formins / microtubule organizing center / integrin-mediated signaling pathway / EGFR downregulation / cytoplasmic ribonucleoprotein granule / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / mitotic spindle / ubiquitin protein ligase activity
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 domain profile. / C2 DOCK-type domain profile. / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain / Dedicator of cytokinesis / DHR-2, Lobe A ...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 domain profile. / C2 DOCK-type domain profile. / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain / Dedicator of cytokinesis / DHR-2, Lobe A / Dedicator of cytokinesis, C-terminal, lobe C / Dedicator of cytokinesis, C-terminal, lobe A / DOCKER domain / Cdc42 / small GTPase Rho family profile. / Small GTPase Rho / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 species||Mus musculus (house mouse)|
Homo sapiens (human)
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.085 Å|
|Authors||Hanawa-Suetsugu, K. / Kukimoto-Niino, M. / Nishizak, T. / Terada, T. / Shirouzu, M. / Fukui, Y. / Yokoyama, S.|
|Citation||Journal: 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.
|Structure viewer||Molecule: |
Downloads & links
A: Dedicator of cytokinesis protein 8
B: Cell division control protein 42 homolog
|Components on special symmetry positions|
|#1: Protein|| |
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|| |
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||#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 %|
|Crystal grow||Temperature: 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
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å|
|Detector||Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2010|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1 Å / Relative weight: 1|
|Reflection||Resolution: 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 shell||Resolution: 2.09→2.16 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.96 / Rsym value: 0.338 / % possible all: 98.4|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 2WM9
Resolution: 2.085→29.679 Å / SU ML: 0.55 / σ(F): 0 / Phase error: 22.44 / Stereochemistry target values: ML
|Solvent computation||Shrinkage 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|
|Refinement step||Cycle: LAST / Resolution: 2.085→29.679 Å|
|Refine LS restraints|
|LS refinement shell|
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
-Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
- Version 3 of the EMDB header file is now the official format.
- The previous official version 1.9 will be removed from the archive.
Related info.:EMDB header
External links:wwPDB to switch to version 3 of the EMDB data model
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi