[English] 日本語
Yorodumi
- EMDB-25153: Human Trio residues 1284-1959 in complex with Rac1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25153
TitleHuman Trio residues 1284-1959 in complex with Rac1
Map dataTrioN-Rac1 complex
Sample
  • Complex: Human Trio residues 1284-1959 in complex with Rac1
    • Protein or peptide: Triple functional domain protein
    • Protein or peptide: Ras-related C3 botulinum toxin substrate 1
  • Ligand: water
Keywordsguanine nucleotide exchange factor / GTPase / dbl homology / pleckstrin homology / signaling protein
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 lamellipodium assembly / regulation of stress fiber 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 / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / positive regulation of focal adhesion assembly / RHOA GTPase cycle / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / 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 / regulation of cell migration / neuron projection morphogenesis / guanyl-nucleotide exchange factor activity / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / actin filament organization / 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 / : / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / Kalirin-like, spectrin repeats / Kalirin, SH3 / : / 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. / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Triple functional domain protein / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsChen C-L / Ravala SK / Bandekar SJ / Cash J / Tesmer JJG
Funding support United States, 2 items
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, 2021-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25153.png

Downloads & links

-
Map

FileDownload / File: emd_25153.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTrioN-Rac1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.8982356 - 6.2453713
Average (Standard dev.)-0.00026100618 (±0.10754663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Human Trio residues 1284-1959 in complex with Rac1

EntireName: Human Trio residues 1284-1959 in complex with Rac1
Components
  • Complex: Human Trio residues 1284-1959 in complex with Rac1
    • Protein or peptide: Triple functional domain protein
    • Protein or peptide: Ras-related C3 botulinum toxin substrate 1
  • Ligand: water

-
Supramolecule #1: Human Trio residues 1284-1959 in complex with Rac1

SupramoleculeName: Human Trio residues 1284-1959 in complex with Rac1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Triple functional domain protein

MacromoleculeName: Triple functional domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.592969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAEEKRKSA RRKEFIMAEL IQTEKAYVRD LRECMDTYLW EMTSGVEEIP PGIVNKELII FGNMQEIYEF HNNIFLKELE KYEQLPEDV GHCFVTWADK FQMYVTYCKN KPDSTQLILE HAGSYFDEIQ QRHGLANSIS SYLIKPVQRI TKYQLLLKEL L TCCEEGKG ...String:
SNAEEKRKSA RRKEFIMAEL IQTEKAYVRD LRECMDTYLW EMTSGVEEIP PGIVNKELII FGNMQEIYEF HNNIFLKELE KYEQLPEDV GHCFVTWADK FQMYVTYCKN KPDSTQLILE HAGSYFDEIQ QRHGLANSIS SYLIKPVQRI TKYQLLLKEL L TCCEEGKG EIKDGLEVML SVPKRANDAM HLSMLEGFDE NIESQGELIL QESFQVWDPK TLIRKGRERH LFLFEMSLVF SK EVKDSSG RSKYLYKSKL FTSELGVTEH VEGDPCKFAL WVGRTPTSDN KIVLKASSIE NKQDWIKHIR EVIQERTIHL KGA LKEPIH IPKTAPATRQ KGRRDGEDLD SQGDGSSQPD TISIASRTSQ NTLDSDKLSG GCELTVVIHD FTACNSNELT IRRG QTVEV LERPHDKPDW CLVRTTDRSP AAEGLVPCGS LCIAHSRSSM EMEGIFNHKD SLSVSSNDAS PPASVASLQP HMIGA QSSP GPKRPGNTLR KWLTSPVRRL SSGKADGHVK KLAHKHKKSR EVRKSADAGS QKDSDDSAAT PQDETVEERG RNEGLS SGT LSKSSSSGMQ SCGEEEGEEG ADAVPLPPPM AIQQHSLLQP DSQDDKASSR LLVRPTSSET PSAAELVSAI EELVKSK MA LEDRPSSLLV DQGDSSSPSF NPSDNSLLSS SSPIDEM

UniProtKB: Triple functional domain protein

-
Macromolecule #2: Ras-related C3 botulinum toxin substrate 1

MacromoleculeName: Ras-related C3 botulinum toxin substrate 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.811453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GEFMQAIKCV VVGDGAVGKT CLLISYTTNA FPGEYIPTVF DNYSANVMVD GKPVNLGLWD TAGQEDYDRL RPLSYPQTDV FLICFSLVS PASFENVRAK WYPEVRHHCP NTPIILVGTK LDLRDDKDTI EKLKEKKLTP ITYPQGLAMA KEIGAVKYLE C SALTQRGL ...String:
GEFMQAIKCV VVGDGAVGKT CLLISYTTNA FPGEYIPTVF DNYSANVMVD GKPVNLGLWD TAGQEDYDRL RPLSYPQTDV FLICFSLVS PASFENVRAK WYPEVRHHCP NTPIILVGTK LDLRDDKDTI EKLKEKKLTP ITYPQGLAMA KEIGAVKYLE C SALTQRGL KTVFDEAIRA VLCPPPVKKR KRKCLLL

UniProtKB: Ras-related C3 botulinum toxin substrate 1

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
200.0 mMNaClSodium Chloride
2.0 mMC4H10O2S2dithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 10.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 0.01 mrad
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number real images: 2817 / Average exposure time: 3.12 sec. / Average electron dose: 55.0 e/Å2
Details: 3514 movies were initially collected. After motion correction and CTF estimation, 697 micrographs were rejected due to poor CTF fitting.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE / Details: Ab-initio model generated from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 922202
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

2nz8

chain_id: A, source_name: PDB, initial_model_type: experimental model

2nz8

chain_id: B, source_name: PDB, initial_model_type: experimental model
DetailsThe 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-7sj4:
Human Trio residues 1284-1959 in complex with Rac1

+
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