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- PDB-7ur2: Crystal structure of the Sec14 domain of the RhoGEF Kalirin -

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Basic information

Entry
Database: PDB / ID: 7ur2
TitleCrystal structure of the Sec14 domain of the RhoGEF Kalirin
ComponentsIsoform 7 of Kalirin
KeywordsLIPID BINDING PROTEIN / Ras homologous guanine nucleotide exchange factor / CRAL-TRIO domain / spectrin repeat / lysophospholipids
Function / homology
Function and homology information


EPHB-mediated forward signaling / maternal process involved in parturition / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / modification of postsynaptic actin cytoskeleton / G alpha (q) signalling events / G alpha (12/13) signalling events / regulation of dendrite development ...EPHB-mediated forward signaling / maternal process involved in parturition / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / modification of postsynaptic actin cytoskeleton / G alpha (q) signalling events / G alpha (12/13) signalling events / regulation of dendrite development / negative regulation of growth hormone secretion / MAPK6/MAPK4 signaling / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / habituation / maternal behavior / neurotransmitter receptor localization to postsynaptic specialization membrane / NMDA selective glutamate receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / extrinsic component of membrane / social behavior / lactation / adult locomotory behavior / axonogenesis / guanyl-nucleotide exchange factor activity / axon guidance / memory / presynapse / nervous system development / postsynaptic density / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / 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 / 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. / Fibronectin type III domain / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 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. / Immunoglobulin-like domain superfamily / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsLi, Y. / Doukov, T.I. / Hao, B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099948 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135592 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK032948 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure of the Sec14 domain of Kalirin reveals a distinct class of lipid-binding module in RhoGEFs.
Authors: Li, Y. / Pustovalova, Y. / Doukov, T.I. / Hoch, J.C. / Mains, R.E. / Eipper, B.A. / Hao, B.
History
DepositionApr 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 7 of Kalirin
B: Isoform 7 of Kalirin
C: Isoform 7 of Kalirin
D: Isoform 7 of Kalirin
E: Isoform 7 of Kalirin
F: Isoform 7 of Kalirin
G: Isoform 7 of Kalirin
H: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,61315
Polymers173,9418
Non-polymers6727
Water25,4371412
1
A: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8392
Polymers21,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8392
Polymers21,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isoform 7 of Kalirin


Theoretical massNumber of molelcules
Total (without water)21,7431
Polymers21,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8392
Polymers21,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9353
Polymers21,7431
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8392
Polymers21,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Isoform 7 of Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8392
Polymers21,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Isoform 7 of Kalirin


Theoretical massNumber of molelcules
Total (without water)21,7431
Polymers21,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.160, 82.420, 83.270
Angle α, β, γ (deg.)81.090, 71.790, 79.880
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Isoform 7 of Kalirin / Protein Duo / Serine/threonine-protein kinase with Dbl- and pleckstrin homology domain


Mass: 21742.564 Da / Num. of mol.: 8 / Fragment: Sec14 domain (UNP residues 2-192)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kalrn / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A2CG49, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, 20-25% PEG3350, 0.2 M sodium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
41001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL14-111.195
SYNCHROTRONSSRL BL12-220.9792
SYNCHROTRONNSLS-II 17-ID-230.9793
SYNCHROTRONNSLS-II 17-ID-140.9201
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJul 9, 2018
DECTRIS PILATUS 6M2PIXELNov 16, 2018
DECTRIS EIGER X 16M3PIXELFeb 15, 2019
DECTRIS EIGER X 9M4PIXELJul 20, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
11.1951
20.97921
30.97931
40.92011
ReflectionResolution: 1.89→78.64 Å / Num. obs: 137673 / % possible obs: 95.9 % / Redundancy: 18.3 % / Biso Wilson estimate: 35.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.015 / Rrim(I) all: 0.063 / Net I/σ(I): 31.6
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 19 % / Rmerge(I) obs: 1.294 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6729 / CC1/2: 0.907 / Rpim(I) all: 0.303 / Rrim(I) all: 1.329 / % possible all: 94

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHENIX1.19.2-4128phasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→61.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6768 4.92 %RANDOM
Rwork0.195 ---
obs0.196 137668 95.9 %-
Displacement parametersBiso max: 261.83 Å2 / Biso mean: 48.49 Å2 / Biso min: 17.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.4352 Å210.4462 Å2-3.061 Å2
2--3.4146 Å2-1.2604 Å2
3----0.9794 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.89→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10652 0 35 1412 12099
Biso mean--137.98 53.57 -
Num. residues----1330
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5215SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1839HARMONIC5
X-RAY DIFFRACTIONt_it11004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1419SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13439SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11004HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14856HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion2.8
LS refinement shellResolution: 1.89→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1965 130 4.72 %
Rwork0.2109 2624 -
all0.2102 2754 -
obs--92.87 %
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)
11.7880.9398-0.56913.1715-0.44171.8603-0.16340.1114-0.0059-0.37330.04170.0363-0.02860.10220.1217-0.0301-0.0328-0.0219-0.12150.0191-0.0857.055579.7672.4744
21.33421.09490.2072.57020.49961.9089-0.04990.09760.0811-0.22610.04280.18930.1581-0.16920.0071-0.0361-0.0301-0.0465-0.10010.0499-0.071250.963929.28476.6382
33.56420.5806-0.37460.7139-0.41480.94040.117-0.37450.24990.1541-0.0758-0.0083-0.07580.1638-0.0412-0.0874-0.02790.0047-0.0345-0.0069-0.061177.226652.182688.3247
42.67581.3415-2.52631.1999-1.10074.3604-0.29680.0828-0.4752-0.1506-0.0398-0.2880.1101-0.22140.3366-0.21960.01250.0585-0.1738-0.03870.065626.703955.699961.9761
51.90590.946-1.23231.2919-0.82112.55070.0344-0.15790.12930.08460.04170.0922-0.0042-0.0933-0.0761-0.09950.01280.0033-0.0244-0.008-0.041812.153752.873816.974
61.60051.56930.54053.39860.52731.60730.1097-0.06480.170.121-0.17840.30790.0921-0.14450.0687-0.0023-0.0289-0.005-0.12650.0034-0.100835.359525.043939.3269
71.70930.8834-1.28213.0791-1.79663.0286-0.21070.2158-0.1545-0.25820.04110.00490.1437-0.22120.1696-0.0749-0.0090.0148-0.1231-0.0686-0.04641.101775.60135.2466
84.07381.2388-0.75131.6088-0.31321.46830.2901-0.46590.22330.2062-0.19-0.0375-0.15770.3672-0.1001-0.061-0.05920.0406-0.0076-0.0281-0.171763.587647.299646.4168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A19 - 192
2X-RAY DIFFRACTION2{ B|* }B19 - 192
3X-RAY DIFFRACTION3{ C|* }C20 - 192
4X-RAY DIFFRACTION4{ D|* }D20 - 192
5X-RAY DIFFRACTION5{ E|* }E20 - 192
6X-RAY DIFFRACTION6{ F|* }F20 - 192
7X-RAY DIFFRACTION7{ G|* }G20 - 192
8X-RAY DIFFRACTION8{ H|* }H20 - 192

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