[English] 日本語
Yorodumi
- PDB-6d8z: Crystal Structure of the C-terminal Guanine Nucleotide Exchange F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d8z
TitleCrystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio
ComponentsTriple functional domain protein
KeywordsSIGNALING PROTEIN / RhoGEF / Dbl Family member / Dbl Homology / Pleckstrin Homology
Function / homology
Function and homology information


cell surface receptor protein tyrosine phosphatase signaling pathway / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / negative regulation of fat cell differentiation / extrinsic component of membrane / postsynaptic modulation of chemical synaptic transmission / presynaptic active zone / NRAGE signals death through JNK / RHOJ GTPase cycle / CDC42 GTPase cycle ...cell surface receptor protein tyrosine phosphatase signaling pathway / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / negative regulation of fat cell differentiation / extrinsic component of membrane / postsynaptic modulation of chemical synaptic transmission / presynaptic active zone / NRAGE signals death through JNK / RHOJ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / cell projection / axon guidance / G alpha (12/13) signalling events / postsynapse / G alpha (q) signalling events / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / ATP binding / cytosol / cytoplasm
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / 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 / Spectrin repeat ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / 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 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 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
Similarity search - Domain/homology
Triple functional domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBandekar, S. / Tesmer, J.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL122416-02z United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL071818 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA221289 United States
CitationJournal: Sci Signal / Year: 2019
Title: Structure of the C-terminal guanine nucleotide exchange factor module of Trio in an autoinhibited conformation reveals its oncogenic potential.
Authors: Bandekar, S.J. / Arang, N. / Tully, E.S. / Tang, B.A. / Barton, B.L. / Li, S. / Gutkind, J.S. / Tesmer, J.J.G.
History
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 25, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triple functional domain protein
B: Triple functional domain protein
C: Triple functional domain protein


Theoretical massNumber of molelcules
Total (without water)112,4473
Polymers112,4473
Non-polymers00
Water46826
1
A: Triple functional domain protein


Theoretical massNumber of molelcules
Total (without water)37,4821
Polymers37,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Triple functional domain protein


Theoretical massNumber of molelcules
Total (without water)37,4821
Polymers37,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Triple functional domain protein


Theoretical massNumber of molelcules
Total (without water)37,4821
Polymers37,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.181, 95.787, 182.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 37482.273 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1960-2275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIO / Plasmid: PMALC2H10T / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / Variant (production host): 1960-2275
References: UniProt: O75962, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / GUANINE EXCHANGE FACTOR MODULE / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 3350, 100MM HEPES PH 7.5, HANGING DROP, 293K, VAPOR DIFFUSION, HANGING DROP
PH range: 7.5

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 30692 / % possible obs: 98.7 % / Redundancy: 5 % / Rsym value: 0.085 / Net I/σ(I): 18.94
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.238 / Num. unique all: 1371 / Rsym value: 0.746 / % possible all: 90.1

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGN

2rgn


Resolution: 2.65→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 39.035 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1504 5 %RANDOM
Rwork0.225 ---
obs0.227 28787 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7499 0 0 26 7525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197641
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.97110258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27623.86386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.425151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0691561
X-RAY DIFFRACTIONr_chiral_restr0.0820.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215683
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4613.3543622
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8385.0284517
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4033.3734019
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.50944.40110685
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 97 -
Rwork0.34 1862 -
obs--89.53 %
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)
15.6369-1.22811.94284.4936-0.916.35720.0512-0.1998-0.668-0.088-0.04670.08250.93370.3084-0.00450.15650.01630.040.4166-0.02320.1008-10.922-7.568-15.865
29.7619-1.09993.6564.4539-0.4318.16720.1393-1.0370.32120.2424-0.0107-0.2611-0.12570.185-0.12860.0283-0.03890.00810.6721-0.08320.05046.3585.3696.342
33.040.2827-0.73784.64782.73836.7288-0.04140.08130.2216-0.2001-0.09120.2164-0.18070.23530.13260.01590.0145-0.01460.43560.05140.0334-20.0819.83117.146
45.8704-0.3905-1.36124.38010.29649.2371-0.0262-0.4283-0.51980.08780.00190.54320.4181-0.50640.02430.1582-0.0497-0.00480.33220.08780.2795-35.566-10.30436.626
56.8416-3.2603-3.21545.01132.83625.97280.18570.35251.189-0.13030.1179-0.4817-0.814-0.6829-0.30360.13290.1228-0.00860.54430.04440.2216-21.10312.049-45.763
65.8659-1.9363-1.67893.85811.58449.03410.08370.0343-0.3072-0.06960.01070.2420.572-0.825-0.09440.0954-0.20020.00070.5582-0.04030.0407-36.209-2.66-23.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1967 - 2142
2X-RAY DIFFRACTION2A2143 - 2273
3X-RAY DIFFRACTION3B1959 - 2146
4X-RAY DIFFRACTION4B2147 - 2272
5X-RAY DIFFRACTION5C1969 - 2146
6X-RAY DIFFRACTION6C2147 - 2273

+
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