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