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- PDB-5o33: A structure of the GEF Kalirin DH1 domain in complex with the sma... -

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Basic information

Entry
Database: PDB / ID: 5o33
TitleA structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1
Components
  • Kalirin
  • Ras-related C3 botulinum toxin substrate 1
KeywordsHYDROLASE / Complex. GEF. Small GTPase
Function / homology
Function and homology information


RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RAC1 GTPase cycle / maternal process involved in parturition / RHOA GTPase cycle / regulation of respiratory burst / modification of postsynaptic actin cytoskeleton / negative regulation of interleukin-23 production ...RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RAC1 GTPase cycle / maternal process involved in parturition / RHOA GTPase cycle / regulation of respiratory burst / modification of postsynaptic actin cytoskeleton / negative regulation of interleukin-23 production / regulation of neutrophil migration / regulation of dendrite development / localization within membrane / NMDA selective glutamate receptor signaling pathway / Activated NTRK2 signals through CDK5 / negative regulation of growth hormone secretion / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / positive regulation of dendritic spine morphogenesis / WNT5:FZD7-mediated leishmania damping / EPHB-mediated forward signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of modification of postsynaptic actin cytoskeleton / cortical cytoskeleton organization / habituation / respiratory burst / hepatocyte growth factor receptor signaling pathway / maternal behavior / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / G alpha (q) signalling events / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / neurotransmitter receptor localization to postsynaptic specialization membrane / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / extrinsic component of membrane / neuromuscular junction development / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / social behavior / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / lactation / cell-matrix adhesion / axonogenesis / cell chemotaxis / adult locomotory behavior / substrate adhesion-dependent cell spreading
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / 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 ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / SH3-RhoGEF linking unstructured region / 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 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Small GTPase Rho / small GTPase Rho family 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type III domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / SH3 domain / Small GTPase / Ras family / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Rab subfamily of small GTPases / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / P-loop containing nucleotide triphosphate hydrolases / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1 / Kalirin
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGray, J. / Krojer, T. / Talon, R. / Fairhead, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P. / von Delft, F.
CitationJournal: To Be Published
Title: A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1
Authors: Gray, J. / Krojer, T. / Talon, R. / Fairhead, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P. / von Delft, F.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
B: Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5839
Polymers40,7672
Non-polymers8167
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-3 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.255, 63.255, 346.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 19710.764 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) / References: UniProt: P63000
#2: Protein Kalirin / / Huntingtin-associated protein-interacting protein / PAM COOH-terminal interactor protein 10 / P- ...Huntingtin-associated protein-interacting protein / PAM COOH-terminal interactor protein 10 / P-CIP10 / Protein Duo / Serine/threonine-protein kinase with Dbl- and pleckstrin homology domain


Mass: 21056.195 Da / Num. of mol.: 1 / Fragment: UNP residues 1253-1432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kalrn, Duo, Hapip / Production host: Escherichia coli (E. coli)
References: UniProt: P97924, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M citrate pH4.2, 0.2M sodium chloride, 18% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.64→57.78 Å / Num. obs: 52137 / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.0971 / Net I/σ(I): 11.21

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NZ8

2nz8


Resolution: 1.64→54.78 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.48
RfactorNum. reflection% reflection
Rfree0.2398 2442 4.95 %
Rwork0.2067 --
obs0.2084 49371 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→54.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 28 24 282 3121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092921
X-RAY DIFFRACTIONf_angle_d1.0723968
X-RAY DIFFRACTIONf_dihedral_angle_d14.3081071
X-RAY DIFFRACTIONf_chiral_restr0.043451
X-RAY DIFFRACTIONf_plane_restr0.005503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6402-1.67370.48631410.43082493X-RAY DIFFRACTION88
1.6737-1.71010.40641180.4132621X-RAY DIFFRACTION92
1.7101-1.74990.47441350.39392561X-RAY DIFFRACTION91
1.7499-1.79360.39811180.36122637X-RAY DIFFRACTION93
1.7936-1.84210.3451450.32962623X-RAY DIFFRACTION93
1.8421-1.89630.35371390.30792692X-RAY DIFFRACTION94
1.8963-1.95750.32521470.29112698X-RAY DIFFRACTION95
1.9575-2.02750.36131500.27162713X-RAY DIFFRACTION95
2.0275-2.10870.32831370.25942786X-RAY DIFFRACTION96
2.1087-2.20470.31311550.23432696X-RAY DIFFRACTION95
2.2047-2.32090.23781430.21552800X-RAY DIFFRACTION97
2.3209-2.46630.25771170.20172814X-RAY DIFFRACTION96
2.4663-2.65670.23751470.20762835X-RAY DIFFRACTION97
2.6567-2.92410.25621510.20352847X-RAY DIFFRACTION97
2.9241-3.34710.22121400.20152921X-RAY DIFFRACTION98
3.3471-4.21680.19731620.16443001X-RAY DIFFRACTION99
4.2168-54.81060.1871970.16713191X-RAY DIFFRACTION99
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)
12.88080.330.23753.4797-0.77330.201-0.06730.05190.1119-0.152-0.1877-0.0831-0.04140.0780.09920.33750.1402-0.07370.2642-0.01670.31361.3091-14.79217.8238
23.07970.79721.58180.9483-0.33721.76230.0777-0.03820.2282-0.196-0.1457-0.2654-0.0015-0.29130.13610.3010.1379-0.00690.39090.02120.49212-7.608518.0962
32.8121-0.6017-0.24042.4852-0.51822.02510.24580.4607-0.3896-0.4295-0.24090.28870.25940.00640.00780.36030.174-0.11260.352-0.07680.3433-6.2186-20.398414.0088
42.9628-0.21121.18883.1164-0.48092.03850.0431-0.216-0.346-0.0885-0.09510.07180.1797-0.051-0.00920.24720.1463-0.00140.2612-0.00750.31534.3515-26.932327.3522
52.0939-0.55330.25832.03961.28782.55990.0330.44870.2739-0.3659-0.0185-0.6319-0.06560.7086-0.03750.28680.20280.03750.32110.01980.339911.1859-18.170818.8198
62.8382-0.34542.46482.59721.0248.6778-0.04920.15880.41990.05870.0868-0.3905-0.53420.5106-0.0720.13280.04320.00660.2649-0.0060.3046-14.0037-1.872618.125
72.26230.3823-1.05341.6622-0.78591.76960.10570.4964-0.9285-1.19740.0980.39380.87020.7406-0.30930.78370.2828-0.12780.9012-0.10250.2579-18.2683-12.0539-8.152
82.4499-1.69270.18192.95630.02573.06450.3050.2022-0.3159-0.1556-0.04240.34870.4292-0.1379-0.1660.19390.036-0.08470.3213-0.00970.3499-22.9513-10.363514.2875
91.96030.9135-0.37710.4567-0.5613.70180.2411.2095-0.1035-0.3950.2071-0.0067-0.1870.24480.07430.7330.45050.15551.2658-0.01460.0607-8.6796-11.414-5.6837
102.1868-1.0973-0.70230.7568-0.07231.10330.40250.2331-0.1026-0.4142-0.09370.09530.08550.4804-0.18870.31440.1347-0.04680.4175-0.07860.2798-11.8999-12.151710.3885
112.61021.13411.13122.99560.92541.9404-0.1215-0.60840.30070.75920.3732-0.13580.0220.1424-0.30150.34990.1594-0.03780.4102-0.00190.3488-15.4574-8.668132.688
122.62671.13461.45772.2976-0.76752.43870.4519-0.4438-0.55650.8833-0.05640.44210.7739-0.7131-0.46940.3349-0.0237-0.05290.4060.10350.4797-23.0968-18.07425.9345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 177 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1232 through 1257 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1258 through 1277 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1278 through 1341 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1342 through 1353 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1354 through 1372 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1373 through 1387 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1388 through 1410 )

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