[English] 日本語
Yorodumi
- PDB-2nz8: N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nz8
TitleN-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1
Components
  • ras-related C3 botulinum toxin substrate 1 isoform Rac1
  • triple functional domain protein
KeywordsSIGNALING PROTEIN / CELL CYCLE / Trio / Rac1 / Dbl-family GEF / Rho-family GTPase / DH/PH cassette
Function / homology
Function and homology information


cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / ruffle assembly / NTRK2 activates RAC1 ...cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / positive regulation of bicellular tight junction assembly / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / Azathioprine ADME / positive regulation of cell-substrate adhesion / positive regulation of neutrophil chemotaxis / Sema4D mediated inhibition of cell attachment and migration / Ephrin signaling / CD28 dependent Vav1 pathway / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / extrinsic component of membrane / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of cell size / negative regulation of fat cell differentiation / positive regulation of Rho protein signal transduction / Rho GDP-dissociation inhibitor binding / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Rac protein signal transduction / RHO GTPases activate PAKs / presynaptic active zone / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / positive regulation of focal adhesion assembly / RHOA GTPase cycle / anatomical structure morphogenesis / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / postsynaptic modulation of chemical synaptic transmission / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / actin filament polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / axon guidance / neuron projection morphogenesis / regulation of cell migration / secretory granule membrane / guanyl-nucleotide exchange factor activity / small monomeric GTPase / actin filament organization / cell-matrix adhesion / Signal transduction by L1 / VEGFR2 mediated vascular permeability / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell chemotaxis / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Kalirin-like, spectrin repeats / Kalirin, SH3 / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Kalirin-like, spectrin repeats / Kalirin, SH3 / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / : / SOS1/NGEF-like PH domain / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Small GTP-binding protein domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Triple functional domain protein / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The DH and PH Domains of Trio Coordinately Engage Rho GTPases for their Efficient Activation
Authors: Chhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J.
History
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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: ras-related C3 botulinum toxin substrate 1 isoform Rac1
B: triple functional domain protein


Theoretical massNumber of molelcules
Total (without water)56,2732
Polymers56,2732
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-11 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.492, 108.558, 53.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2175-

HOH

21B-2221-

HOH

DetailsThere is one biological unit in each assymetric unit (complex between Rac1 and Trio DH/PH)

-
Components

#1: Protein ras-related C3 botulinum toxin substrate 1 isoform Rac1 / Ras-related C3 botulinum toxin substrate 1 / p21-Rac1 / Ras-like protein TC25


Mass: 19710.764 Da / Num. of mol.: 1 / Fragment: soluble part (residues 1-177)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63000
#2: Protein triple functional domain protein / PTPRF-interacting protein


Mass: 36561.953 Da / Num. of mol.: 1 / Fragment: N-terminal DH/PH cassette (residues 1226-1535)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIO / Plasmid: pPROEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O75962
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 100 mM sodium cacodylate pH 5.5 to 6.5, 14 to 18% (w/v) PEG 8000, and 300-500 mM calcium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2004
RadiationMonochromator: double crystal Si (220) cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 39574 / Num. obs: 39416 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.069 / Χ2: 1.824 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.53 / Num. unique all: 3903 / Rsym value: 0.524 / Χ2: 1.124 / % possible all: 99.8

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å31 Å
Translation3 Å31 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE

1nty

1foe


Resolution: 2→19.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.565 / SU ML: 0.111 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1968 5.1 %RANDOM
Rwork0.223 ---
obs0.225 38900 99.61 %-
all-39416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 0 242 3905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223737
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9735043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0785451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69824.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14915696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5851517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022767
X-RAY DIFFRACTIONr_nbd_refined0.190.21729
X-RAY DIFFRACTIONr_nbtor_refined0.30.22539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.214
X-RAY DIFFRACTIONr_mcbond_it0.521.52359
X-RAY DIFFRACTIONr_mcangle_it0.84823679
X-RAY DIFFRACTIONr_scbond_it1.2631584
X-RAY DIFFRACTIONr_scangle_it1.9134.51364
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 129 -
Rwork0.261 2718 -
obs-2847 99.89 %
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)
11.74430.1444-0.80492.44270.23784.6849-0.04960.0714-0.0816-0.33550.0723-0.12130.31950.0851-0.0227-0.1328-0.0171-0.0041-0.19020.0069-0.197148.08532.129-7.1214
22.506-0.0472-0.26733.5037-0.23851.87320.0028-0.19390.05130.33340.0504-0.01880.06790.0635-0.0531-0.1602-0.03940.0117-0.1770-0.242144.310841.100815.5037
330.0993-1.859313.347412.5573-1.669514.3882.9268-1.1897-5.89470.3162-0.0338-0.01822.5485-0.6843-2.8930.2877-0.2386-0.6478-0.02720.31161.207532.252511.864214.9497
41.1617-0.2572-0.46922.30930.52972.3013-0.0079-0.01120.0247-0.06610.03370.19270.0196-0.0923-0.0258-0.0604-0.0114-0.0088-0.08330.0335-0.056841.964637.17424.9849
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1771 - 177
22BB1231 - 14119 - 189
33BB1412 - 1417190 - 195
43BB1423 - 1434201 - 212
53BB1449 - 1497227 - 275
63BB1505 - 1535283 - 313
74A - BC - D2000 - 2241

+
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