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- PDB-2rmk: Rac1/PRK1 Complex -

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Basic information

Entry
Database: PDB / ID: 2rmk
TitleRac1/PRK1 Complex
Components
  • Ras-related C3 botulinum toxin substrate 1
  • Serine/threonine-protein kinase N1
KeywordsMEMBRANE PROTEIN/TRANSFERASE / G protein / effector / ADP-ribosylation / Alternative splicing / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Polymorphism / Prenylation / ATP-binding / Cytoplasm / Kinase / Phosphorylation / Serine/threonine-protein kinase / Transferase / MEMBRANE PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


epithelial cell migration / 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 / protein kinase C / auditory receptor cell morphogenesis ...epithelial cell migration / 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 / protein kinase C / 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 / diacylglycerol-dependent serine/threonine kinase activity / Activated NTRK2 signals through CDK5 / interneuron migration / regulation of hydrogen peroxide metabolic process / kinocilium / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / ruffle assembly / renal system process / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / cochlea morphogenesis / 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 / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / regulation of cell motility / histone H3T11 kinase activity / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / cell projection assembly / B cell apoptotic process / positive regulation of bicellular tight junction assembly / ruffle organization / regulation of lamellipodium assembly / thioesterase binding / regulation of germinal center formation / regulation of stress fiber assembly / negative regulation of fibroblast migration / regulation of neuron migration / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / RHO GTPases activate KTN1 / regulation of immunoglobulin production / Activation of RAC1 / regulation of androgen receptor signaling pathway / MET activates RAP1 and RAC1 / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / Azathioprine ADME / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / positive regulation of cell-substrate adhesion / positive regulation of neutrophil chemotaxis / Wnt signaling pathway, planar cell polarity pathway / superoxide anion generation / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / nuclear androgen receptor binding / RHOB GTPase cycle / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Activation of RAC1 downstream of NMDARs / negative regulation of B cell proliferation / dendrite morphogenesis / Rho GDP-dissociation inhibitor binding / RHOC GTPase cycle / regulation of cell size / synaptic transmission, GABAergic / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / establishment or maintenance of cell polarity / pericentriolar material / positive regulation of actin filament polymerization / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / B cell homeostasis / cleavage furrow / ficolin-1-rich granule membrane / regulation of postsynapse assembly / Sema3A PAK dependent Axon repulsion
Similarity search - Function
Serine/threonine-protein kinase N1, second HR1 domain / HR1 repeat / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal ...Serine/threonine-protein kinase N1, second HR1 domain / HR1 repeat / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Small GTPase Rho / Small GTPase Rho domain profile. / C2 domain / C2 domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 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 / Helix Hairpins / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 1 / Serine/threonine-protein kinase N1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsModha, R. / Campbell, L.J. / Nietlispach, D. / Buhecha, H.R. / Owen, D. / Mott, H.R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Rac1 Polybasic Region Is Required for Interaction with Its Effector PRK1
Authors: Modha, R. / Campbell, L.J. / Nietlispach, D. / Buhecha, H.R. / Owen, D. / Mott, H.R.
History
DepositionOct 25, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
B: Serine/threonine-protein kinase N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0264
Polymers30,4812
Non-polymers5462
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 21463.143 Da / Num. of mol.: 1 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#2: Protein Serine/threonine-protein kinase N1 / PRK1_HR1b / Protein kinase C-like 1 / Protein-kinase C-related kinase 1 / Protein kinase C-like PKN ...PRK1_HR1b / Protein kinase C-like 1 / Protein-kinase C-related kinase 1 / Protein kinase C-like PKN / Serine-threonine protein kinase N / Protein kinase PKN-alpha


Mass: 9017.416 Da / Num. of mol.: 1 / Fragment: HR1b domain, REM 2, UNP residues 122-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKN1, PKN, PRK1, PRKCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16512, protein kinase C
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1323D 13C-edited
14213C-separated NOESY
1533D 1H-15N NOESY
1643D 1H-13C NOESY
1743D 13C-edited
18413C-separated NOESY
1953D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM [U-13C; U-15N; U-2H] Rac1; 0.6mM PRK1 HR1b; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM [U-100% 13C; U-100% 15N] Rac1; 0.6mM PRK1 HR1b; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O90% H2O/10% D2O
30.6mM [U-100% 15N] Rac1; 0.6mM PRK1 HR1b; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O90% H2O/10% D2O
40.6mM [U-100% 13C; U-100% 15N] Rac1; 0.6mM PRK1 Rac1; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O90% H2O/10% D2O
50.6mM [U-100% 15N] HR1b; 0.6mM PRK1 Rac1; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRac1[U-13C; U-15N; U-2H]1
0.6 mMPRK1 HR1b1
0.7 mMPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER1
0.6 mMRac1[U-100% 13C; U-100% 15N]2
0.6 mMPRK1 HR1b2
0.7 mMPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER2
0.6 mMRac1[U-100% 15N]3
0.6 mMPRK1 HR1b3
0.7 mMPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER3
0.6 mMHR1b[U-100% 13C; U-100% 15N]4
0.6 mMPRK1 Rac14
0.7 mMPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER4
0.6 mMHR1b[U-100% 15N]5
0.6 mMPRK1 Rac15
0.7 mMPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER5
Sample conditionsIonic strength: 0.225 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
Azara2.7Boucherprocessing
ANSIGKraulischemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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