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- PDB-2wkp: Structure of a photoactivatable Rac1 containing Lov2 Wildtype -

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Basic information

Entry
Database: PDB / ID: 2wkp
TitleStructure of a photoactivatable Rac1 containing Lov2 Wildtype
ComponentsNPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsTRANSFERASE / CELL ADHESION / GTPASE / SMALL G-PROTEIN / RHO FAMILY / RAS SUPERFAMILY LOV2 / ATP-BINDING / LIGHT-INDUCED SIGNAL TRANSDUCTION / LOV2 / PHOTOTROPIN1 / NUCLEOTIDE-BINDING PROTEIN ENGINEERING / PROTEIN DESIGN / CHIMERA
Function / homology
Function and homology information


embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation ...embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / interneuron migration / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / blue light photoreceptor activity / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / cochlea morphogenesis / regulation of hydrogen peroxide metabolic process / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / positive regulation of skeletal muscle acetylcholine-gated channel clustering / ruffle organization / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / GTP-dependent protein binding / positive regulation of bicellular tight junction assembly / cell projection assembly / thioesterase binding / regulation of lamellipodium assembly / negative regulation of fibroblast migration / regulation of neuron migration / regulation of stress fiber assembly / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / Nef and signal transduction / hepatocyte growth factor receptor signaling pathway / PCP/CE pathway / Activation of RAC1 / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / quinolinate biosynthetic process / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / Wnt signaling pathway, planar cell polarity pathway / superoxide anion generation / regulation of receptor signaling pathway via JAK-STAT / lamellipodium assembly / NRAGE signals death through JNK / positive regulation of ruffle assembly / dendrite morphogenesis / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / synaptic transmission, GABAergic / pericentriolar material / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Rac protein signal transduction / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / RHO GTPases activate PKNs / phagocytic cup / positive regulation of lamellipodium assembly / positive regulation of stress fiber assembly / cell projection / RAC1 GTPase cycle / actin filament polymerization
Similarity search - Function
PAS domain / Small GTPase Rho / PAS-associated, C-terminal / PAC domain profile. / Small GTPase Rho domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain ...PAS domain / Small GTPase Rho / PAS-associated, C-terminal / PAC domain profile. / Small GTPase Rho domain 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 / PAS domain superfamily / 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 / 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: 1.9 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_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

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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)38,6475
Polymers37,6031
Non-polymers1,0444
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.880, 113.880, 69.520
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 / RAC1_HUMAN / P21-RAC1 / RAS-LIKE PROTEIN TC25 / CELL MIGRATION-INDUCING GENE 5 PROTEIN


Mass: 37602.984 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 , 5 types, 317 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-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


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLU 91 TO HIS ...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 CA ACETATE, 100 MM SODIUM CACODYLATE PH 5.5, 12 % (W/V) PEG 8000

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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: 1.9→50 Å / Num. obs: 41136 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 20.59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.7 / % possible all: 99.6

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Processing

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

1mh1

2vou


Resolution: 1.9→40.221 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 2037 4.9 %
Rwork0.1658 --
obs0.1673 41133 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.155 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.5869 Å20 Å2-0 Å2
2--1.5869 Å20 Å2
3----3.1739 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 65 313 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092743
X-RAY DIFFRACTIONf_angle_d1.1963756
X-RAY DIFFRACTIONf_dihedral_angle_d19.1721044
X-RAY DIFFRACTIONf_chiral_restr0.085427
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.27691350.21462570X-RAY DIFFRACTION100
1.9442-1.99280.20911340.19082607X-RAY DIFFRACTION100
1.9928-2.04670.21161360.17552561X-RAY DIFFRACTION100
2.0467-2.10690.21321320.16882571X-RAY DIFFRACTION100
2.1069-2.17490.19741300.16932577X-RAY DIFFRACTION100
2.1749-2.25260.19921340.16532589X-RAY DIFFRACTION100
2.2526-2.34280.25381350.16782605X-RAY DIFFRACTION100
2.3428-2.44940.22311380.17042564X-RAY DIFFRACTION100
2.4494-2.57860.2281360.17612634X-RAY DIFFRACTION100
2.5786-2.74010.23551370.17012591X-RAY DIFFRACTION100
2.7401-2.95160.19451360.17992614X-RAY DIFFRACTION100
2.9516-3.24850.17781350.16812616X-RAY DIFFRACTION100
3.2485-3.71830.15941410.15112626X-RAY DIFFRACTION100
3.7183-4.68350.14831380.13512649X-RAY DIFFRACTION100
4.6835-40.22980.18831400.16032722X-RAY DIFFRACTION99

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