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- PDB-5wi4: CRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH ARHGEF2 -

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Basic information

Entry
Database: PDB / ID: 5wi4
TitleCRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH ARHGEF2
ComponentsDynein light chain Tctex-type 1,Rho guanine nucleotide exchange factor 2
KeywordsMOTOR PROTEIN / DYNEIN LIGHT CHAIN / RHO GEF / CARGO TRANSPORT
Function / homology
Function and homology information


negative regulation of podosome assembly / guanyl-nucleotide exchange factor activity => GO:0005085 / guanyl-nucleotide exchange factor activity => GO:0005085 / : / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / secretory vesicle / NRAGE signals death through JNK / : / G alpha (12/13) signalling events ...negative regulation of podosome assembly / guanyl-nucleotide exchange factor activity => GO:0005085 / guanyl-nucleotide exchange factor activity => GO:0005085 / : / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / secretory vesicle / NRAGE signals death through JNK / : / G alpha (12/13) signalling events / asymmetric neuroblast division / cellular response to muramyl dipeptide / positive regulation of neuron migration / GTP-dependent protein binding / negative regulation of microtubule depolymerization / regulation of G protein-coupled receptor signaling pathway / regulation of Rho protein signal transduction / cytoplasmic dynein complex / podosome / postsynaptic density, intracellular component / establishment of mitotic spindle orientation / cytoskeletal motor activity / bicellular tight junction / cytoplasmic microtubule / axonal growth cone / positive regulation of neuron differentiation / photoreceptor inner segment / Neutrophil degranulation / dendritic shaft / actin filament organization / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of neuron projection development / spindle / ruffle membrane / negative regulation of neurogenesis / positive regulation of interleukin-6 production / G-protein beta-subunit binding / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / lamellipodium / cell body / positive regulation of NF-kappaB transcription factor activity / growth cone / cytoplasmic vesicle / microtubule binding / vesicle / microtubule / postsynaptic density / cytoskeleton / intracellular signal transduction / cell division / innate immune response / neuronal cell body / glutamatergic synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / ARHGEF2, PH domain / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain ...Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / ARHGEF2, PH domain / ARHGEF1-like, PH domain / PH domain / 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Dynein light chain Tctex-type 1 / Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBalan, M. / Ishiyama, N. / Marshall, C.B. / Ikura, M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Cancer Research Society (CRS)CRS 14014 Canada
Canada Foundation for Innovation Canada
CitationJournal: Sci Signal / Year: 2017
Title: MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity.
Authors: Sandi, M.J. / Marshall, C.B. / Balan, M. / Coyaud, E. / Zhou, M. / Monson, D.M. / Ishiyama, N. / Chandrakumar, A.A. / La Rose, J. / Couzens, A.L. / Gingras, A.C. / Raught, B. / Xu, W. / ...Authors: Sandi, M.J. / Marshall, C.B. / Balan, M. / Coyaud, E. / Zhou, M. / Monson, D.M. / Ishiyama, N. / Chandrakumar, A.A. / La Rose, J. / Couzens, A.L. / Gingras, A.C. / Raught, B. / Xu, W. / Ikura, M. / Morrison, D.K. / Rottapel, R.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain Tctex-type 1,Rho guanine nucleotide exchange factor 2
B: Dynein light chain Tctex-type 1,Rho guanine nucleotide exchange factor 2
C: Dynein light chain Tctex-type 1,Rho guanine nucleotide exchange factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3937
Polymers47,0083
Non-polymers3844
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, DYNLT1-ARHGEF2 chimera runs as a dimer in gel filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-84 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.967, 91.967, 83.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-228-

HOH

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Components

#1: Protein Dynein light chain Tctex-type 1,Rho guanine nucleotide exchange factor 2 / Activator of G-protein signaling 2 / AGS2 / T-complex testis-specific protein 1 / TCTEX-1 / Guanine ...Activator of G-protein signaling 2 / AGS2 / T-complex testis-specific protein 1 / TCTEX-1 / Guanine nucleotide exchange factor H1 / GEF-H1 / LBC'S first cousin / Lymphoid blast crisis-like 1 / Oncogene LFC / Rhobin


Mass: 15669.433 Da / Num. of mol.: 3 / Fragment: unp residue 1-113; unp residues 139-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Dynlt1, Tctel1, Tctex-1, Tctex1, Arhgef2, Kiaa0651, Lbcl1, Lfc
Plasmid: PGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P51807, UniProt: Q60875
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.33M AMMONIUM SULPHATE, 0.25MM SODIUM MALONATE, 7.2MM CALCIUM CHLORIDE
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27423 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 31.492
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 6.578 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
Coot(0.7)phasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YGT

1ygt


Resolution: 2→36.83 Å / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 27.87
RfactorNum. reflection% reflection
Rfree0.21 2010 7.33 %
Rwork0.174 --
obs0.176 27423 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→36.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 20 178 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072874
X-RAY DIFFRACTIONf_angle_d1.0433897
X-RAY DIFFRACTIONf_dihedral_angle_d13.688983
X-RAY DIFFRACTIONf_chiral_restr0.068473
X-RAY DIFFRACTIONf_plane_restr0.003474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04860.23341370.21571703X-RAY DIFFRACTION88
2.0486-2.1040.25761400.20661741X-RAY DIFFRACTION89
2.104-2.16590.21961430.20421766X-RAY DIFFRACTION89
2.1659-2.23580.20571390.19881785X-RAY DIFFRACTION90
2.2358-2.31570.23221360.20031780X-RAY DIFFRACTION91
2.3157-2.40840.25311410.20521795X-RAY DIFFRACTION91
2.4084-2.5180.23131450.20171787X-RAY DIFFRACTION91
2.518-2.65070.2371400.19381822X-RAY DIFFRACTION92
2.6507-2.81670.26281430.19791821X-RAY DIFFRACTION92
2.8167-3.03410.23361430.18681829X-RAY DIFFRACTION93
3.0341-3.33930.1851450.16471857X-RAY DIFFRACTION93
3.3393-3.8220.16321440.14471880X-RAY DIFFRACTION93
3.822-4.81370.17831430.12831879X-RAY DIFFRACTION93
4.8137-36.83730.20581520.16931962X-RAY DIFFRACTION93

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