[English] 日本語
Yorodumi
- PDB-3b13: Crystal structure of the DHR-2 domain of DOCK2 in complex with Ra... -

+
Open data


ID or keywords:

Loading...

-
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 / myeloid dendritic cell activation involved in immune response / alpha-beta T cell proliferation / establishment of T cell polarity / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development ...membrane raft polarization / myeloid dendritic cell activation involved in immune response / alpha-beta T cell proliferation / establishment of T cell polarity / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / macropinocytosis / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / immunological synapse formation / interneuron migration / kinocilium / regulation of hydrogen peroxide metabolic process / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / cochlea morphogenesis / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative thymic T cell selection / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / ruffle organization / myoblast fusion / regulation of lamellipodium assembly / positive thymic T cell selection / thioesterase binding / regulation of neuron migration / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / sphingosine-1-phosphate receptor signaling pathway / motor neuron axon guidance / Nef and signal transduction / PCP/CE pathway / RHO GTPases activate KTN1 / Activation of RAC1 / MET activates RAP1 and RAC1 / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / Azathioprine ADME / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / positive regulation of cell-substrate adhesion / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Activation of RAC1 downstream of NMDARs / dendrite morphogenesis / Rho GDP-dissociation inhibitor binding / regulation of cell size / positive regulation of Rho protein signal transduction / synaptic transmission, GABAergic / positive regulation of dendritic spine development / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Rac protein signal transduction / pericentriolar material / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / regulation of postsynapse assembly / ficolin-1-rich granule membrane / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / regulation of neuronal synaptic plasticity / RHOA GTPase cycle / positive regulation of focal adhesion assembly
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 / Dedicator of cytokinesis (DOCK) TPR region / Dedicator of cytokinesis / C2 DOCK-type domain ...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 / Dedicator of cytokinesis (DOCK) TPR region / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / Variant SH3 domain / Small GTPase Rho / Small GTPase Rho domain 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
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

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

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

Read more