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- PDB-5hzh: Crystal structure of photoinhibitable Rac1 containing C450A mutan... -

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Basic information

Entry
Database: PDB / ID: 5hzh
TitleCrystal structure of photoinhibitable Rac1 containing C450A mutant LOV2 domain
ComponentsRas-related C3 botulinum toxin substrate 1,NPH1-1,Ras-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / Photoswitch / Chimera
Function / homology
Function and homology information


regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / blue light photoreceptor activity ...regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / blue light photoreceptor activity / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / regulation of hydrogen peroxide metabolic process / engulfment of apoptotic cell / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / cell projection assembly / respiratory burst / motor neuron axon guidance / ruffle organization / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / negative regulation of fibroblast migration / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate CIT / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / superoxide anion generation / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / regulation of nitric oxide biosynthetic process / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / forebrain development / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / ficolin-1-rich granule membrane / regulation of postsynapse assembly / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / regulation of synaptic vesicle endocytosis / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / positive regulation of stress fiber assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / substrate adhesion-dependent cell spreading / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / cell projection / positive regulation of substrate adhesion-dependent cell spreading / actin filament polymerization / RAC1 GTPase cycle / cell-matrix adhesion / EPHB-mediated forward signaling / regulation of cell migration / positive regulation of endothelial cell migration / secretory granule membrane / actin filament organization / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Signal transduction by L1 / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / small monomeric GTPase / FCGR3A-mediated phagocytosis / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell chemotaxis / FCERI mediated MAPK activation / trans-Golgi network / neuron migration / negative regulation of receptor-mediated endocytosis
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / Small GTPase Rho / 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 / PAS-associated, C-terminal / PAC domain profile. / Small GTPase Rho / 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 speciesHomo sapiens (human)
Avena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTarnawski, M. / Dagliyan, O. / Chu, P.H. / Shirvanyants, D. / Dokholyan, N.V. / Hahn, K.M. / Schlichting, I.
CitationJournal: Science / Year: 2016
Title: Engineering extrinsic disorder to control protein activity in living cells.
Authors: Dagliyan, O. / Tarnawski, M. / Chu, P.H. / Shirvanyants, D. / Schlichting, I. / Dokholyan, N.V. / Hahn, K.M.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
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

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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,NPH1-1,Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1506
Polymers37,0661
Non-polymers1,0845
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-29 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.050, 74.270, 58.400
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ras-related C3 botulinum toxin substrate 1,NPH1-1,Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 37066.254 Da / Num. of mol.: 1 / Mutation: Q61L,Q61L,Q61L,Q61L,Q61L,Q61L,Q61L,Q61L,Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Avena sativa (oats)
Gene: RAC1, TC25, MIG5, NPH1-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, UniProt: O49003

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Non-polymers , 5 types, 32 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.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M calcium acetate, 26% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97885 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9516 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WKQ

2wkq


Resolution: 2.6→37.135 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 28.14
RfactorNum. reflection% reflection
Rfree0.2553 476 5.01 %
Rwork0.2037 --
obs0.2063 9506 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 66 27 2622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022643
X-RAY DIFFRACTIONf_angle_d0.613594
X-RAY DIFFRACTIONf_dihedral_angle_d13.029988
X-RAY DIFFRACTIONf_chiral_restr0.023407
X-RAY DIFFRACTIONf_plane_restr0.003452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.97610.29731570.24292994X-RAY DIFFRACTION100
2.9761-3.7490.26841580.21342990X-RAY DIFFRACTION100
3.749-37.13880.23641610.18733046X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.50360.87231.25071.69890.38171.63190.20730.8068-0.9330.25450.2636-0.24020.23470.43370.69470.3350.0711-0.02670.3573-0.09210.41218.0649-15.540620.0128
20.56530.31610.40910.2310.18430.30850.05190.04420.12740.3105-0.3494-0.33380.16620.0393-00.561-0.03980.01820.61270.06410.492316.23452.639311.4368
30.51910.2063-0.16971.75970.35871.63350.0043-0.14840.02450.08230.0339-0.2121-0.06570.1102-00.2562-0.0168-0.00520.3590.02680.30442.569524.59982.4478
42.3034-0.0340.34351.641-0.14591.82850.0828-0.1688-0.08360.0936-0.03590.0681-0.00210.09050.01490.2316-0.01580.00960.1363-0.0090.203510.5887-10.417625.867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 327 )

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