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- PDB-2qme: Crystal structure of human RAC3 in complex with CRIB domain of hu... -

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Entry
Database: PDB / ID: 2qme
TitleCrystal structure of human RAC3 in complex with CRIB domain of human p21-activated kinase 1 (PAK1)
Components
  • CRIB domain of the Serine/threonine-protein kinase PAK 1
  • Ras-related C3 botulinum toxin substrate 3
KeywordsSIGNALING PROTEIN/TRANSFERASE / GTPase RAC3 / small GTP binding protein / p21 rac / ras-related C3 botulinum toxin substrate 3 / signaling protein / CRIB / kinase / Structural Genomics / Structural Genomics Consortium / SGC / Cell projection / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation / Allosteric enzyme / ATP-binding / Phosphorylation / Serine/threonine-protein kinase / Transferase / Apoptosis / Cell junction / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


cerebral cortex GABAergic interneuron development / negative regulation of cell proliferation involved in contact inhibition / regulation of neuron maturation / protein localization to cytoplasmic stress granule / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / positive regulation of microtubule nucleation / engulfment of apoptotic cell / NADPH oxidase complex / respiratory burst ...cerebral cortex GABAergic interneuron development / negative regulation of cell proliferation involved in contact inhibition / regulation of neuron maturation / protein localization to cytoplasmic stress granule / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / positive regulation of microtubule nucleation / engulfment of apoptotic cell / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / cell projection assembly / synaptic transmission, GABAergic / motor neuron axon guidance / PCP/CE pathway / Activation of RAC1 / positive regulation of cell adhesion mediated by integrin / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway / RHOV GTPase cycle / establishment or maintenance of cell polarity / branching morphogenesis of an epithelial tube / regulation of axonogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / Rac protein signal transduction / RHOJ GTPase cycle / exocytosis / RHOQ GTPase cycle / filamentous actin / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / CDC42 GTPase cycle / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / neuromuscular process controlling balance / RHOH GTPase cycle / Generation of second messenger molecules / intercalated disc / Smooth Muscle Contraction / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / endomembrane system / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / homeostasis of number of cells within a tissue / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / ruffle / collagen binding / EPHB-mediated forward signaling / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / phosphorylation / cell chemotaxis / neuron projection morphogenesis / small monomeric GTPase / VEGFR2 mediated vascular permeability / G protein activity / Signal transduction by L1 / actin filament organization / cell periphery / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / Wnt signaling pathway / ruffle membrane / Z disc / calcium-dependent protein binding / cell-cell junction / cell migration / positive regulation of peptidyl-serine phosphorylation / lamellipodium / chromosome / regulation of cell shape / growth cone / actin cytoskeleton organization / cytoplasmic vesicle / nuclear membrane / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / neuron projection / chromatin remodeling / positive regulation of protein phosphorylation / axon / protein phosphorylation
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 3 / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsUgochukwu, E. / Yang, X. / Elkins, J.M. / Burgess-Brown, N. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. ...Ugochukwu, E. / Yang, X. / Elkins, J.M. / Burgess-Brown, N. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of the human RAC3 in complex with the CRIB domain of human p21-activated kinase 1 (PAK1).
Authors: Ugochukwu, E. / Yang, X. / Elkins, J.M. / Burgess-Brown, N. / Bunkoczi, G. / Knapp, S. / Doyle, D.
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 3
I: CRIB domain of the Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7286
Polymers23,9982
Non-polymers7304
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
MethodPISA
2
A: Ras-related C3 botulinum toxin substrate 3
I: CRIB domain of the Serine/threonine-protein kinase PAK 1
hetero molecules

A: Ras-related C3 botulinum toxin substrate 3
I: CRIB domain of the Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,45612
Polymers47,9974
Non-polymers1,4598
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.226, 53.480, 47.682
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-511-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

#1: Protein Ras-related C3 botulinum toxin substrate 3 / p21-Rac3


Mass: 19934.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P60763
#2: Protein/peptide CRIB domain of the Serine/threonine-protein kinase PAK 1 / p21-activated kinase 1 / PAK-1 / p65-PAK / Alpha-PAK


Mass: 4063.479 Da / Num. of mol.: 1 / Fragment: CRIB domain / Source method: obtained synthetically
Details: Synthetic peptide with the sequence of the CRIB domain of human PAK1 protein
References: UniProt: Q13153, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 242 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 2 M (NH4)2S04, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→47.62 Å / Num. all: 21448 / Num. obs: 21448 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 27.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4 / Rsym value: 0.343 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G0N

2g0n


Resolution: 1.75→47.62 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.899 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19177 1100 5.1 %RANDOM
Rwork0.14893 ---
all0.15114 20345 --
obs0.15114 20345 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.02 Å2
2--0.59 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 45 238 1843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221663
X-RAY DIFFRACTIONr_bond_other_d0.0020.021095
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9962273
X-RAY DIFFRACTIONr_angle_other_deg0.88432681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21524.05869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61215258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.228158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
X-RAY DIFFRACTIONr_nbd_refined0.2020.2336
X-RAY DIFFRACTIONr_nbd_other0.2020.21182
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2816
X-RAY DIFFRACTIONr_nbtor_other0.0850.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2168
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.230
X-RAY DIFFRACTIONr_mcbond_it3.51751051
X-RAY DIFFRACTIONr_mcbond_other1.2865405
X-RAY DIFFRACTIONr_mcangle_it4.29571644
X-RAY DIFFRACTIONr_scbond_it6.1759728
X-RAY DIFFRACTIONr_scangle_it7.43511628
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 86 -
Rwork0.194 1481 -
obs--99.18 %
Refinement TLS params.Method: refined / Origin x: -12.6483 Å / Origin y: 12.2223 Å / Origin z: 13.6153 Å
111213212223313233
T-0.0315 Å2-0.0033 Å20.0029 Å2--0.0232 Å2-0.0003 Å2---0.0216 Å2
L0.4667 °20.0262 °20.1486 °2-0.5499 °20.3052 °2--0.9467 °2
S-0.0004 Å °0.0249 Å °-0.0318 Å °0.0024 Å °0.0498 Å °-0.0251 Å °-0.0216 Å °0.0492 Å °-0.0494 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1782 - 179
2X-RAY DIFFRACTION1IB10 - 331 - 24

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