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- PDB-1nf3: Structure of Cdc42 in a complex with the GTPase-binding domain of... -

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Basic information

Entry
Database: PDB / ID: 1nf3
TitleStructure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6
Components
  • G25K GTP-binding protein, placental isoform
  • PAR-6B
KeywordsSIGNALING PROTEIN / semi-CRIB motif / Switch I and II / PDZ domain / GTPase binding domain
Function / homology
Function and homology information


Tight junction interactions / RHOV GTPase cycle / regulation of cellular localization / 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 ...Tight junction interactions / RHOV GTPase cycle / regulation of cellular localization / 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 / 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 / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / centrosome cycle / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / 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 / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / bicellular tight junction / 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 / 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 / filopodium / 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 / G beta:gamma signalling through CDC42 / cytoplasmic ribonucleoprotein granule / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation
Similarity search - Function
Partitioning defective protein 6, PB1 domain / Cdc42 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Small GTPase Rho / small GTPase Rho family profile. / PDZ domain / Pdz3 Domain ...Partitioning defective protein 6, PB1 domain / Cdc42 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Small GTPase Rho / small GTPase Rho family profile. / PDZ domain / Pdz3 Domain / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rab subfamily of small GTPases / PDZ superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / Partitioning defective 6 homolog beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGarrard, S.M. / Capaldo, C.T. / Gao, L. / Rosen, M.K. / Macara, I.G. / Tomchick, D.R.
Citation
Journal: Embo J. / Year: 2003
Title: Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6
Authors: Garrard, S.M. / Capaldo, C.T. / Gao, L. / Rosen, M.K. / Macara, I.G. / Tomchick, D.R.
#1: Journal: Curr.Biol. / Year: 2002
Title: Assembly of epithelial tight junctions is negatively regulated by Par6
Authors: Gao, L. / Joberty, G. / Macara, I.G.
#2: Journal: Nat.Cell Biol. / Year: 2000
Title: The cell-polarity protein Par6 links Par3 and atypical protein kinase C to Cdc42
Authors: Joberty, G. / Petersen, C. / Gao, L. / Macara, I.G.
#3: Journal: Nat.Cell Biol. / Year: 2000
Title: A mammalian Par-3-Par-6 complex implicated in Cdc42/Rac1 and aPKC signalling and cell polarity
Authors: Lin, D. / Edwards, A.S. / Fawcett, J.P. / Mbamalu, G. / Scott, J.D. / Pawson, T.
#4: Journal: Curr.Biol. / Year: 2000
Title: A human homolog of the C. elegans polarity determinant Par-6 links Rac and Cdc42 to PKCzeta signaling and cell transformation
Authors: Qiu, R.G. / Abo, A. / Steven Martin, G.
#5: Journal: DEVELOPMENT / Year: 1996
Title: Par-6, a gene involved in the establishment of asymmetry in early C. elegans embryos, mediates the asymmetric localization of Par-3
Authors: Watts, J.L. / Etemad-Moghadam, B. / Guo, S. / Boyd, L. / Draper, B.W. / Mello, C.C. / Priess, J.R. / Kemphues, K.J.
History
DepositionDec 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G25K GTP-binding protein, placental isoform
B: G25K GTP-binding protein, placental isoform
C: PAR-6B
D: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5788
Polymers71,4854
Non-polymers1,0934
Water7,620423
1
A: G25K GTP-binding protein, placental isoform
C: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2894
Polymers35,7422
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-29 kcal/mol
Surface area16400 Å2
MethodPISA
2
B: G25K GTP-binding protein, placental isoform
D: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2894
Polymers35,7422
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-29 kcal/mol
Surface area16200 Å2
MethodPISA
3
A: G25K GTP-binding protein, placental isoform
C: PAR-6B
hetero molecules

B: G25K GTP-binding protein, placental isoform
D: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5788
Polymers71,4854
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area7170 Å2
ΔGint-61 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.744, 53.787, 79.521
Angle α, β, γ (deg.)81.55, 76.59, 90.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein G25K GTP-binding protein, placental isoform / GP / CDC42 homolog


Mass: 21566.949 Da / Num. of mol.: 2 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60953
#2: Protein PAR-6B


Mass: 14175.417 Da / Num. of mol.: 2 / Fragment: GTPase-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Par6B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JK83
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.27 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 24% PEG 4000, 100mM sodium citrate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris1droppH8.5
31 mM1dropMgCl2
40.100 mMGMPPNP1drop
510 mMbeta-mercaptoethanol1drop
624 %PEG40001reservoir
7100 mMsodium citrate1reservoirpH6.4
80.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 8, 2002 / Details: double crystal monochromator
RadiationMonochromator: graphite double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→40.5 Å / Num. all: 38985 / Num. obs: 38985 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 80223
Reflection shell
*PLUS
% possible obs: 87.1 % / Rmerge(I) obs: 0.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NGR

2ngr


Resolution: 2.1→29.17 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1733 5 %RANDOM
Rwork0.219 ---
all0.219 34917 --
obs0.219 34917 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2756 Å2 / ksol: 0.35546 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.63 Å2-3.7 Å2
2---5.93 Å2-0.45 Å2
3---4.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å-
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å-
Refinement stepCycle: LAST / Resolution: 2.1→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 66 423 5395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 165 4.9 %
Rwork0.265 3173 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMLIGANDS.TOP
X-RAY DIFFRACTION4LIGANDS.PARAMION.TOP
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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