[English] 日本語
Yorodumi
- PDB-7sj4: Human Trio residues 1284-1959 in complex with Rac1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sj4
TitleHuman Trio residues 1284-1959 in complex with Rac1
Components
  • Ras-related C3 botulinum toxin substrate 1
  • Triple functional domain protein
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor / GTPase / dbl homology / pleckstrin homology
Function / homology
Function and homology information


cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis ...cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / regulation of hydrogen peroxide metabolic process / engulfment of apoptotic cell / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / cell projection assembly / respiratory burst / motor neuron axon guidance / ruffle organization / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / negative regulation of fibroblast migration / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate CIT / regulation of small GTPase mediated signal transduction / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / forebrain development / superoxide anion generation / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / regulation of nitric oxide biosynthetic process / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / negative regulation of fat cell differentiation / extrinsic component of membrane / regulation of receptor signaling pathway via JAK-STAT / presynaptic active zone / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / RHOJ GTPase cycle / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / Rac protein signal transduction / CDC42 GTPase cycle / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ficolin-1-rich granule membrane / regulation of postsynapse assembly / RAC3 GTPase cycle / positive regulation of focal adhesion assembly / RHOA GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate NADPH Oxidases / regulation of synaptic vesicle endocytosis / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / postsynaptic modulation of chemical synaptic transmission / RHO GTPases activate IQGAPs / positive regulation of stress fiber assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / substrate adhesion-dependent cell spreading / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / cell projection / neuron projection morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / actin filament polymerization / RAC1 GTPase cycle / cell-matrix adhesion / EPHB-mediated forward signaling / regulation of cell migration / positive regulation of endothelial cell migration / axon guidance / guanyl-nucleotide exchange factor activity / secretory granule membrane
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 ...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 domain 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Small GTP-binding protein domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Roll / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Triple functional domain protein / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsChen, C.-L. / Ravala, S.K. / Bandekar, S.J. / Cash, J. / Tesmer, J.J.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA221289 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31CA224804 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Structural/functional studies of Trio provide insights into its configuration and show that conserved linker elements enhance its activity for Rac1.
Authors: Sumit J Bandekar / Chun-Liang Chen / Sandeep K Ravala / Jennifer N Cash / Larisa V Avramova / Mariya V Zhalnina / J Silvio Gutkind / Sheng Li / John J G Tesmer /
Abstract: Trio is a large and highly conserved metazoan signaling scaffold that contains two Dbl family guanine nucleotide exchange factor (GEF) modules, TrioN and TrioC, selective for Rac and RhoA GTPases, ...Trio is a large and highly conserved metazoan signaling scaffold that contains two Dbl family guanine nucleotide exchange factor (GEF) modules, TrioN and TrioC, selective for Rac and RhoA GTPases, respectively. The GEF activities of TrioN and TrioC are implicated in several cancers, especially uveal melanoma. However, little is known about how these modules operate in the context of larger fragments of Trio. Here we show via negative stain electron microscopy that the N-terminal region of Trio is extended and could thus serve as a rigid spacer between the N-terminal putative lipid-binding domain and TrioN, whereas the C-terminal half of Trio seems globular. We found that regions C-terminal to TrioN enhance its Rac1 GEF activity and thus could play a regulatory role. We went on to characterize a minimal, well-behaved Trio fragment with enhanced activity, Trio, in complex with Rac1 using cryo-electron microscopy and hydrogen-deuterium exchange mass spectrometry and found that the region conferring enhanced activity is disordered. Deletion of two different strongly conserved motifs in this region eliminated this enhancement, suggesting that they form transient intramolecular interactions that promote GEF activity. Because Dbl family RhoGEF modules have been challenging to directly target with small molecules, characterization of accessory Trio domains such as these may provide alternate routes for the development of therapeutics that inhibit Trio activity in human cancer.
History
DepositionOct 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triple functional domain protein
B: Ras-related C3 botulinum toxin substrate 1


Theoretical massNumber of molelcules
Total (without water)97,4042
Polymers97,4042
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Triple functional domain protein / PTPRF-interacting protein


Mass: 75592.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: O75962, non-specific serine/threonine protein kinase
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 21811.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P63000
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human Trio residues 1284-1959 in complex with Rac1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta (DE3) pLysS
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)C8H18N2O4S1
2200 mMSodium ChlorideNaCl1
32 mMdithiothreitolC4H10O2S21
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot force 10

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 0.01 mradians
Image recordingAverage exposure time: 3.12 sec. / Electron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 2817
Details: 3514 movies were initially collected. After motion correction and CTF estimation, 697 micrographs were rejected due to poor CTF fitting.
Image scansWidth: 11520 / Height: 8184 / Movie frames/image: 40

-
Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2Leginonimage acquisition
4cryoSPARC3.3.1CTF correction
7UCSF Chimera1.15model fitting
8Coot9.6model fitting
10Coot9.6model refinement
11PHENIX1.20-4459model refinement
12cryoSPARC3.3.1initial Euler assignment
13cryoSPARC3.3.1final Euler assignment
14cryoSPARC3.3.1classification
15cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 922202 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Details: The initial model was generated from the pdb structure (2NZ8) using the SWISS-MODEL server and rigid-body fitted using Chimera. Several runs of structure refinement were done using the coot ...Details: The initial model was generated from the pdb structure (2NZ8) using the SWISS-MODEL server and rigid-body fitted using Chimera. Several runs of structure refinement were done using the coot and phenix real-space refinement.
Atomic model building

3D fitting-ID: 1 / Accession code: 2NZ8 / Initial refinement model-ID: 1 / PDB-ID: 2NZ8

2nz8

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023964
ELECTRON MICROSCOPYf_angle_d0.4145350
ELECTRON MICROSCOPYf_dihedral_angle_d9.5631502
ELECTRON MICROSCOPYf_chiral_restr0.041593
ELECTRON MICROSCOPYf_plane_restr0.003681

+
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