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Basic information

Entry
Database: PDB / ID: 2odb
TitleThe crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Components
  • Human Cell Division Cycle 42 (CDC42)
  • Serine/threonine-protein kinase PAK 6
KeywordsPROTEIN BINDING / small GTPase / CRIB / kinase / protein-protein complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity ...GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / 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 / neuron projection arborization / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHOD GTPase cycle / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / Activation of RAC1 / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / neuron projection extension / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / positive regulation of DNA replication / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / locomotory behavior / filopodium / learning / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization
Similarity search - Function
Serine/threonine-protein kinase PAK 6 / 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 family profile. ...Serine/threonine-protein kinase PAK 6 / 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 family 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Cell division control protein 42 homolog / Serine/threonine-protein kinase PAK 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUgochukwu, E. / Yang, X. / Elkins, J. / Soundararajan, M. / Pike, A.C.W. / Eswaran, J. / Burgess, N. / Debreczeni, J.E. / Sundstrom, M. / Arrowsmith, C. ...Ugochukwu, E. / Yang, X. / Elkins, J. / Soundararajan, M. / Pike, A.C.W. / Eswaran, J. / Burgess, N. / Debreczeni, J.E. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Gileadi, O. / von Delft, F. / Knapp, S. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Authors: Yang, X. / Ugochukwu, E. / Elkins, J. / Soundararajan, M. / Eswaran, J. / Pike, A.C.W. / Burgess, N. / Debreczeni, J.E. / Gileadi, O. / Knapp, S. / Doyle, D.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: 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 / struct_site
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_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.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
Remark 999sequence The sequence of human CDC42 isoform 1 is not available in uniprot database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3068
Polymers25,4372
Non-polymers8696
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-69 kcal/mol
Surface area10740 Å2
MethodPISA
2
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,61316
Polymers50,8744
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area8820 Å2
ΔGint-183 kcal/mol
Surface area19930 Å2
MethodPISA
3
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,61316
Polymers50,8744
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area9490 Å2
ΔGint-168 kcal/mol
Surface area19270 Å2
MethodPISA
4
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,61316
Polymers50,8744
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area9840 Å2
ΔGint-152 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.366, 162.366, 45.968
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-201-

SO4

DetailsOne monomer of each protein in the asymmetric unit

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Human Cell Division Cycle 42 (CDC42)


Mass: 21370.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P60953
#2: Protein/peptide Serine/threonine-protein kinase PAK 6 / p21-activated kinase 6 / PAK-6


Mass: 4066.510 Da / Num. of mol.: 1 / Fragment: PAK6 CRIB domain / Source method: obtained synthetically / References: UniProt: Q9NQU5

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Non-polymers , 5 types, 50 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M acetate, 2M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97956
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 2.4→40.59 Å / Num. obs: 14484 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 / Rsym value: 0.071
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.502 / Rsym value: 0.502 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GRN

1grn


Resolution: 2.4→40.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.923 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23184 732 5.1 %RANDOM
Rwork0.2034 ---
all0.20484 13737 --
obs0.20484 13737 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.158 Å2
Baniso -1Baniso -2Baniso -3
1--4.96 Å2-2.48 Å20 Å2
2---4.96 Å20 Å2
3---7.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 49 44 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221711
X-RAY DIFFRACTIONr_bond_other_d0.0010.021099
X-RAY DIFFRACTIONr_angle_refined_deg1.46622348
X-RAY DIFFRACTIONr_angle_other_deg0.9232713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34125.22467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.291154
X-RAY DIFFRACTIONr_chiral_restr0.0780.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
X-RAY DIFFRACTIONr_nbd_refined0.2010.2283
X-RAY DIFFRACTIONr_nbd_other0.1820.21064
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2817
X-RAY DIFFRACTIONr_nbtor_other0.0860.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4961.51109
X-RAY DIFFRACTIONr_mcbond_other0.0831.5417
X-RAY DIFFRACTIONr_mcangle_it0.79221736
X-RAY DIFFRACTIONr_scbond_it1.2843716
X-RAY DIFFRACTIONr_scangle_it1.9654.5612
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
Rfree0.364 48 -
Rwork0.297 984 -
obs--100 %
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)
13.981.05480.26363.4947-0.04772.10670.1415-0.27291.00780.5026-0.14870.4553-0.19940.00920.0072-0.0814-0.07540.1025-0.2307-0.08330.138913.9842-63.2942-3.8227
27.8741.7819-0.83822.1767-0.68440.22720.06960.4965-0.5417-0.0323-0.0084-0.49110.12990.2255-0.0612-0.0889-0.035-0.0129-0.0786-0.0153-0.208814.0796-77.4512-15.826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1783 - 179
2X-RAY DIFFRACTION2BB11 - 451 - 35

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