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- PDB-5upk: CDC42 binds PAK4 via an extended GTPase-effector interface - 3 pe... -

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Basic information

Entry
Database: PDB / ID: 5upk
TitleCDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide: PAK4cat, PAK4-N45, CDC42
Components
  • (Serine/threonine-protein kinase PAK ...) x 2
  • Cell division control protein 42 homolog
KeywordsTRANSFERASE / GTPase / Kinase / CRIB
Function / homology
Function and homology information


GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination ...GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / dendritic spine development / cadherin binding involved in cell-cell adhesion / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / Activation of RAC1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / RHOV GTPase cycle / phagocytosis, engulfment / nuclear migration / small GTPase-mediated signal transduction / regulation of mitotic nuclear division / Myogenesis / heart contraction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / establishment of cell polarity / RHOQ GTPase cycle / Golgi organization / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / macrophage differentiation / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / negative regulation of endothelial cell apoptotic process / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / RAC1 GTPase cycle / cytoskeleton organization / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament organization / cellular response to starvation / small monomeric GTPase / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / adherens junction / filopodium / regulation of cell growth / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / positive regulation of angiogenesis / apical part of cell / G beta:gamma signalling through CDC42 / mitotic spindle / ubiquitin protein ligase activity / cell-cell junction / intracellular protein localization
Similarity search - Function
Cdc42 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / Small GTPase Rho domain profile. ...Cdc42 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Serine/threonine-protein kinase PAK 4 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHa, B.H. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: CDC42 binds PAK4 via an extended GTPase-effector interface.
Authors: Ha, B.H. / Boggon, T.J.
History
DepositionFeb 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
B: Serine/threonine-protein kinase PAK 4
C: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5596
Polymers65,5063
Non-polymers1,0533
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.465, 61.621, 85.791
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Serine/threonine-protein kinase PAK ... , 2 types, 2 molecules AB

#1: Protein/peptide Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 5653.328 Da / Num. of mol.: 1 / Fragment: UNP residues 1-45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Variant: isoform2 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILP
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 39123.133 Da / Num. of mol.: 1 / Fragment: UNP residues 109-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Variant: isoform2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILP
References: UniProt: O96013, non-specific serine/threonine protein kinase

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Protein , 1 types, 1 molecules C

#3: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 20729.787 Da / Num. of mol.: 1 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P60953

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Non-polymers , 4 types, 28 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 22% PEG1,000 / PH range: 7.0-8.0 / Temp details: R/T

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24144 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.163 / Rsym value: 0.163 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.6 % / CC1/2: 0.311 / Rpim(I) all: 0.912 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIJ

4fij


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 25.02 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26364 1097 4.6 %RANDOM
Rwork0.2179 ---
obs0.22023 22941 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.109 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-1.48 Å2
2--0.33 Å20 Å2
3---1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 56 25 4070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194133
X-RAY DIFFRACTIONr_bond_other_d0.0020.024021
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9965616
X-RAY DIFFRACTIONr_angle_other_deg0.90139271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36923.829175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3171528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02899
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.254.4582012
X-RAY DIFFRACTIONr_mcbond_other1.254.4572011
X-RAY DIFFRACTIONr_mcangle_it2.2246.6782508
X-RAY DIFFRACTIONr_mcangle_other2.2236.6782509
X-RAY DIFFRACTIONr_scbond_it1.1774.7012121
X-RAY DIFFRACTIONr_scbond_other1.1694.6972118
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0826.983106
X-RAY DIFFRACTIONr_long_range_B_refined4.03251.4464393
X-RAY DIFFRACTIONr_long_range_B_other4.02851.3614384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 68 -
Rwork0.296 1661 -
obs--97.96 %
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)
17.8517-3.1906-3.70693.24172.98955.0475-0.10050.3972-0.68330.2045-0.53430.45620.021-0.68530.63480.0758-0.0391-0.0090.161-0.12320.1446-25.537821.792634.0583
21.69970.12191.48021.0670.96612.6362-0.1207-0.0634-0.1994-0.12620.26490.0111-0.08660.0932-0.14410.1605-0.0451-0.06370.07970.01760.07358.914313.001313.9198
32.3235-0.2636-1.57743.31190.9744.94090.1057-0.06840.0907-0.0893-0.4485-0.0591-1.06660.50580.34280.2758-0.1069-0.13220.287-0.02910.123-15.549633.375132.314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 43
2X-RAY DIFFRACTION2B300 - 352
3X-RAY DIFFRACTION2B353 - 411
4X-RAY DIFFRACTION2B412 - 588
5X-RAY DIFFRACTION3C2 - 65
6X-RAY DIFFRACTION3C66 - 92
7X-RAY DIFFRACTION3C93 - 121
8X-RAY DIFFRACTION3C122 - 179

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