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- PDB-6d8z: Crystal Structure of the C-terminal Guanine Nucleotide Exchange F... -

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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 / extrinsic component of membrane / NRAGE signals death through JNK / negative regulation of fat cell differentiation / RHOJ GTPase cycle / presynaptic active zone / CDC42 GTPase cycle / RHOG GTPase cycle ...cell surface receptor protein tyrosine phosphatase signaling pathway / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / extrinsic component of membrane / NRAGE signals death through JNK / negative regulation of fat cell differentiation / RHOJ GTPase cycle / presynaptic active zone / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / postsynaptic modulation of chemical synaptic transmission / RAC1 GTPase cycle / axon guidance / neuron projection morphogenesis / guanyl-nucleotide exchange factor activity / cell projection / G alpha (12/13) signalling events / G alpha (q) signalling events / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / 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 / 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 / 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 / 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 / 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 / Mainly Beta / Mainly Alpha
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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