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- PDB-5qqd: PanDDA analysis group deposition -- Crystal Structure of Kalirin/... -

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Basic information

Entry
Database: PDB / ID: 5qqd
TitlePanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with Z56880342
Components
  • Kalirin
  • Ras-related C3 botulinum toxin substrate 1
KeywordsHydrolase/Transferase / SGC - Diamond I04-1 fragment screening / XChemExplorer / Hydrolase-Transferase complex
Function / homology
Function and homology information


regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / regulation of hydrogen peroxide metabolic process / NADPH oxidase complex / Rac protein signal transduction / negative regulation of receptor-mediated endocytosis ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / regulation of hydrogen peroxide metabolic process / NADPH oxidase complex / Rac protein signal transduction / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / Rho GDP-dissociation inhibitor binding / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / RHO GTPases activate CIT / RHO GTPases activate KTN1 / ruffle organization / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / thioesterase binding / regulation of stress fiber assembly / sphingosine-1-phosphate receptor signaling pathway / cell projection assembly / Wnt signaling pathway, planar cell polarity pathway / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / regulation of lamellipodium assembly / positive regulation of Rho protein signal transduction / Activation of RAC1 / regulation of small GTPase mediated signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / semaphorin-plexin signaling pathway / lamellipodium assembly / CD28 dependent Vav1 pathway / Activation of RAC1 downstream of NMDARs / regulation of cell size / NRAGE signals death through JNK / positive regulation of lamellipodium assembly / DSCAM interactions / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / RHOA GTPase cycle / RHOG GTPase cycle / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / RHO GTPases activate IQGAPs / EPH-ephrin mediated repulsion of cells / positive regulation of substrate adhesion-dependent cell spreading / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ephrin receptor signaling pathway / regulation of actin cytoskeleton organization / extrinsic component of membrane / positive regulation of stress fiber assembly / RHO GTPases activate PKNs / neuron migration / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / G protein activity / substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / regulation of cell migration / cell-matrix adhesion / small monomeric GTPase / actin filament polymerization / cell motility / guanyl-nucleotide exchange factor activity / G alpha (12/13) signalling events / VEGFR2 mediated vascular permeability / actin filament organization / secretory granule membrane / vesicle-mediated transport / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Signal transduction by L1 / positive regulation of endothelial cell migration / cell projection / central nervous system development / cytoplasmic ribonucleoprotein granule / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / axon guidance / FCGR3A-mediated phagocytosis / trans-Golgi network
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / Divergent CRAL/TRIO domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain superfamily / CRAL-TRIO lipid binding domain / Spectrin repeat / Spectrin repeat ...Rho GDP/GTP exchange factor Kalirin/TRIO / Divergent CRAL/TRIO domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain superfamily / CRAL-TRIO lipid binding domain / Spectrin repeat / Spectrin repeat / small GTPase Rho family profile. / Small GTPase Rho / Spectrin/alpha-actinin / Spectrin repeats / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / RhoGEF domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Immunoglobulin I-set domain / Immunoglobulin I-set / PH domain / Fibronectin type III domain / PH domain profile. / Pleckstrin homology domain. / Rho (Ras homology) subfamily of Ras-like small GTPases / Pleckstrin homology domain / Small GTPase / Ras family / 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 / Small GTP-binding protein domain / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / P-loop containing nucleotide triphosphate hydrolases / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea / Kalirin / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.91 Å
AuthorsGray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Gray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)41,3044
Polymers41,0722
Non-polymers2312
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-8 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.836, 62.836, 342.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 19797.844 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 / Protein Duo / Serine/threonine-protein kinase ...Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine-protein kinase with Dbl- and pleckstrin homology domain


Mass: 21274.471 Da / Num. of mol.: 1 / Mutation: None
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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-JGA / N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea


Mass: 169.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.38 Å3/Da / Density % sol: 48.25 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M bis-tris pH 5.5 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.91→342.64 Å / Num. obs: 32694 / % possible obs: 100 % / Redundancy: 33.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.514 / Rpim(I) all: 0.087 / Rrim(I) all: 0.521 / Net I/σ(I): 10.4 / Num. measured all: 1106790 / Scaling rejects: 2217
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.91-1.9618.42.6914306823380.7730.6422.7681.3
8.54-342.6429.70.081524851410.0140.08223.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5O33
Resolution: 1.91→57.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.2 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1633 5 %RANDOM
Rwork0.2059 ---
obs0.2085 30853 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.69 Å2 / Biso mean: 35.516 Å2 / Biso min: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å2-0 Å2
2--0.96 Å2-0 Å2
3----3.12 Å2
Refinement stepCycle: final / Resolution: 1.91→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 16 339 3128
Biso mean--49.67 47.26 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132881
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172641
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.6493919
X-RAY DIFFRACTIONr_angle_other_deg1.3911.5756120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19523.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0981511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_mcbond_it2.7983.7231443
X-RAY DIFFRACTIONr_mcbond_other2.7973.7231444
X-RAY DIFFRACTIONr_mcangle_it4.0475.5751804
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 117 -
Rwork0.347 2176 -
all-2293 -
obs--97.99 %

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