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- PDB-2wkq: Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant -

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Basic information

Entry
Database: PDB / ID: 2wkq
TitleStructure of a photoactivatable Rac1 containing the Lov2 C450A Mutant
ComponentsNPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsTRANSFERASE / CELL ADHESION / NUCLEOTIDE-BINDING / PROTEIN ENGINEERING / RAS SUPERFAMILY LOV2 / PHOTOTROPIN1 / PROTEIN DESIGN / SMALL G-PROTEIN / LIGHT- INDUCED SIGNAL TRANSDUCTION / LOV2 / GTPASE / RHO FAMILY / ATP-BINDING / CHIMERA / NUCLEOTIDE-BINDING PROTEIN ENGINEERING / LIGHT-INDUCED SIGNAL TRANSDUCTION / ALTERNATIVE SPLICING / CELL MEMBRANE / ADP-RIBOSYLATION / LIPOPROTEIN / GTP-BINDING
Function / homology
Function and homology information


regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / blue light photoreceptor activity / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / blue light photoreceptor activity / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / respiratory burst / hepatocyte growth factor receptor signaling pathway / 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 / PCP/CE pathway / regulation of nitric oxide biosynthetic process / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / Azathioprine ADME / Activation of RAC1 / positive regulation of neutrophil chemotaxis / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / DSCAM interactions / establishment or maintenance of cell polarity / 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 / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / 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 / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of microtubule polymerization / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / cell chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / positive regulation of endothelial cell migration / G protein activity / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway / response to wounding / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer
Similarity search - Function
PAS-associated, C-terminal / PAS domain / PAC domain profile. / Small GTPase Rho / small GTPase Rho family profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain ...PAS-associated, C-terminal / PAS domain / PAC domain profile. / Small GTPase Rho / small GTPase Rho family profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PAS domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-TRIPHOSPHATE / non-specific serine/threonine protein kinase / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesAVENA SATIVA (oats)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M.
CitationJournal: Nature / Year: 2009
Title: A Genetically Encoded Photoactivatable Rac Controls the Motility of Living Cells.
Authors: Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M.
History
DepositionJun 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8059
Polymers37,5711
Non-polymers1,2348
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.638, 112.638, 69.306
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1 / RAS-LIKE PROTEIN TC25 / CELL MIGRATION-INDUCING GENE 5 PROTEIN


Mass: 37570.918 Da / Num. of mol.: 1
Fragment: NPH1-1 RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVENA SATIVA (oats), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL10 GOLD / References: UniProt: O49003, UniProt: P63000

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Non-polymers , 6 types, 405 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 450 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, CYS 450 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLU 91 TO HIS ENGINEERED RESIDUE IN CHAIN A, ASN 92 TO HIS

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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: 3.46 Å3/Da / Density % sol: 64.5 % / Description: NONE
Crystal growDetails: 100 MM POTASSIUM CHLORIDE, 5% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001
DetectorType: MARRESEARCH MX-225 / Detector: CCD / Date: Sep 26, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 66895 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 15.4 % / Biso Wilson estimate: 18.79 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.5
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASER1.3.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MH1, 2VOU

1mh1

2vou


Resolution: 1.6→39.887 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 3310 4.9 %
Rwork0.1686 --
obs0.1695 66891 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.895 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.9567 Å20 Å2-0 Å2
2--1.9567 Å20 Å2
3----3.9133 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 75 397 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092746
X-RAY DIFFRACTIONf_angle_d1.3113755
X-RAY DIFFRACTIONf_dihedral_angle_d19.2171049
X-RAY DIFFRACTIONf_chiral_restr0.085425
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62290.20441380.19232636X-RAY DIFFRACTION99
1.6229-1.64710.20761380.18082612X-RAY DIFFRACTION100
1.6471-1.67280.21921380.17832623X-RAY DIFFRACTION100
1.6728-1.70030.20071370.18172614X-RAY DIFFRACTION99
1.7003-1.72960.20111400.17142652X-RAY DIFFRACTION100
1.7296-1.7610.21951350.17712597X-RAY DIFFRACTION100
1.761-1.79490.21861340.16912612X-RAY DIFFRACTION100
1.7949-1.83150.181340.16922632X-RAY DIFFRACTION100
1.8315-1.87140.20061350.16862634X-RAY DIFFRACTION100
1.8714-1.91490.21311360.17672665X-RAY DIFFRACTION100
1.9149-1.96280.18851350.16682603X-RAY DIFFRACTION100
1.9628-2.01580.19211360.16332640X-RAY DIFFRACTION100
2.0158-2.07520.1771370.16322646X-RAY DIFFRACTION100
2.0752-2.14210.19781360.16542632X-RAY DIFFRACTION100
2.1421-2.21870.24061370.16492644X-RAY DIFFRACTION100
2.2187-2.30750.18991380.16482655X-RAY DIFFRACTION100
2.3075-2.41250.16791390.16562660X-RAY DIFFRACTION100
2.4125-2.53970.20321380.16442642X-RAY DIFFRACTION100
2.5397-2.69880.19951380.17192662X-RAY DIFFRACTION100
2.6988-2.90710.18641390.17492652X-RAY DIFFRACTION100
2.9071-3.19950.17641410.172681X-RAY DIFFRACTION100
3.1995-3.66220.15831410.15642679X-RAY DIFFRACTION100
3.6622-4.6130.15191430.14772713X-RAY DIFFRACTION100
4.613-39.89910.17791470.16862795X-RAY DIFFRACTION100

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