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- PDB-8c7d: Structure of the GEF Kalirin DH2 Domain -

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Basic information

Entry
Database: PDB / ID: 8c7d
TitleStructure of the GEF Kalirin DH2 Domain
ComponentsKalirin
KeywordsSIGNALING PROTEIN / GTPase exchange factor / helical bundle
Function / homology
Function and homology information


regulation of small GTPase mediated signal transduction / extrinsic component of membrane / NRAGE signals death through JNK / RHOG GTPase cycle / RHOA GTPase cycle / ephrin receptor signaling pathway / vesicle-mediated transport / EPHB-mediated forward signaling / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity ...regulation of small GTPase mediated signal transduction / extrinsic component of membrane / NRAGE signals death through JNK / RHOG GTPase cycle / RHOA GTPase cycle / ephrin receptor signaling pathway / vesicle-mediated transport / EPHB-mediated forward signaling / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / axon guidance / MAPK6/MAPK4 signaling / G alpha (12/13) signalling events / actin cytoskeleton / nervous system development / G alpha (q) signalling events / postsynaptic density / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion 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 ...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 / 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. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsCallens, M.C. / Thompson, A.P. / Gray, J.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Other private
Alzheimers Research UK (ARUK) United Kingdom
CitationJournal: to be published
Title: Structure-based alignment and analysis of RHO selectivity of RHO-DBL GTPase exchange factors
Authors: Callens, M.C. / Thompson, A.P. / Gray, J.L. / von Delft, F. / Brennan, P.E.
History
DepositionJan 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kalirin


Theoretical massNumber of molelcules
Total (without water)24,0601
Polymers24,0601
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.324, 74.478, 100.121
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Kalirin / Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine-protein kinase ...Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine-protein kinase with Dbl- and pleckstrin homology domain


Mass: 24059.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KALRN, DUET, DUO, HAPIP, TRAD / Production host: Escherichia coli (E. coli)
References: UniProt: O60229, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% W/V PEG3350, 0.1 M succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 18, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.86→59.76 Å / Num. obs: 17994 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.9976 / Rpim(I) all: 0.076 / Rrim(I) all: 0.261 / Net I/σ(I): 7.1
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 881 / CC1/2: 0.351 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→59.76 Å / SU ML: 0.3656 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 907 5.09 %
Rwork0.2273 16924 -
obs0.2298 17831 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.86 Å2
Refinement stepCycle: LAST / Resolution: 1.86→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 0 72 1584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881581
X-RAY DIFFRACTIONf_angle_d0.92972145
X-RAY DIFFRACTIONf_chiral_restr0.0536240
X-RAY DIFFRACTIONf_plane_restr0.0077277
X-RAY DIFFRACTIONf_dihedral_angle_d4.8611219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.980.40081400.3882706X-RAY DIFFRACTION97.1
1.98-2.130.36011400.30042784X-RAY DIFFRACTION99.59
2.13-2.340.29561460.25452769X-RAY DIFFRACTION99.76
2.34-2.680.3081490.23062818X-RAY DIFFRACTION99.83
2.68-3.380.30131740.21892842X-RAY DIFFRACTION99.97
3.38-59.760.22161580.19393005X-RAY DIFFRACTION99.87

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