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- PDB-4js0: Complex of Cdc42 with the CRIB-PR domain of IRSp53 -

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Basic information

Entry
Database: PDB / ID: 4js0
TitleComplex of Cdc42 with the CRIB-PR domain of IRSp53
Components
  • Brain-specific angiogenesis inhibitor 1-associated protein 2
  • Cell division control protein 42 homolog
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN / GTPase binding domain / CRIB domain / cytoskeleton regulation / SIGNALING PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


neuron projection branch point / dendritic spine cytoplasm / 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 ...neuron projection branch point / dendritic spine cytoplasm / 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 / actin crosslink formation / plasma membrane organization / 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 / cadherin binding involved in cell-cell adhesion / regulation of filopodium assembly / leading edge membrane / cytoskeletal anchor activity / positive regulation of dendritic spine morphogenesis / neuropilin signaling pathway / regulation of modification of postsynaptic actin cytoskeleton / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / protein localization to synapse / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / cellular response to L-glutamate / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / neuron projection terminus / embryonic heart tube development / proline-rich region binding / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of mitotic nuclear division / nuclear migration / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / positive regulation of cytokinesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / RHOJ GTPase cycle / positive regulation of actin filament polymerization / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / dendrite development / RHOU GTPase cycle / actin filament bundle assembly / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / excitatory synapse / positive regulation of excitatory postsynaptic potential / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / postsynaptic cytosol / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / postsynaptic density, intracellular component / presynaptic cytosol / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / axonogenesis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule / cellular response to epidermal growth factor stimulus / actin filament organization / transcription coregulator binding / dendritic shaft / small monomeric GTPase / integrin-mediated signaling pathway / PDZ domain binding / filopodium
Similarity search - Function
I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Cdc42 / AH/BAR domain superfamily / Variant SH3 domain / Small GTPase Rho ...I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Cdc42 / AH/BAR domain superfamily / Variant SH3 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / BAR/IMD domain-containing adapter protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKast, D.J. / Dominguez, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Mechanism of IRSp53 inhibition and combinatorial activation by Cdc42 and downstream effectors.
Authors: Kast, D.J. / Yang, C. / Disanza, A. / Boczkowska, M. / Madasu, Y. / Scita, G. / Svitkina, T. / Dominguez, R.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 42 homolog
B: Brain-specific angiogenesis inhibitor 1-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7408
Polymers23,1062
Non-polymers1,6346
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-33 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.230, 67.230, 79.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-322-

HOH

31A-420-

HOH

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Components

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

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


Mass: 19816.783 Da / Num. of mol.: 1 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60953
#2: Protein/peptide Brain-specific angiogenesis inhibitor 1-associated protein 2 / BAI-associated protein 2 / BAI1-associated protein 2 / Protein BAP2 / Fas ligand-associated factor ...BAI-associated protein 2 / BAI1-associated protein 2 / Protein BAP2 / Fas ligand-associated factor 3 / FLAF3 / Insulin receptor substrate p53/p58 / IRS-58 / IRSp53/58 / Insulin receptor substrate protein of 53 kDa / IRSp53 / Insulin receptor substrate p53


Mass: 3288.875 Da / Num. of mol.: 1 / Fragment: CRIB-PR domain / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQB8

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Non-polymers , 4 types, 157 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-20% PEG 4000, 0.2M magnesium chloride, 0.004M betain hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9769 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 15019 / Num. obs: 15019 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.8 %
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 18.4 % / % possible all: 100

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Processing

Software
NameVersionClassification
JDirector(Rigaku)data collection
PHENIXPhaser-MRmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXPhaser-MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.296 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 754 5.04 %
Rwork0.1456 --
obs0.1481 14959 99.84 %
all-14959 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 61 151 1806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151745
X-RAY DIFFRACTIONf_angle_d1.6892397
X-RAY DIFFRACTIONf_dihedral_angle_d17.174663
X-RAY DIFFRACTIONf_chiral_restr0.082275
X-RAY DIFFRACTIONf_plane_restr0.007295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04690.2211540.16132747X-RAY DIFFRACTION99
2.0469-2.25290.22861450.14182783X-RAY DIFFRACTION100
2.2529-2.57880.18781610.14232816X-RAY DIFFRACTION100
2.5788-3.24860.2051410.15062836X-RAY DIFFRACTION100
3.2486-34.30190.18571530.14213023X-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)
11.04670.1111-0.22962.0030.41621.75180.0751-0.2878-0.17210.0996-0.0042-0.31830.08850.2539-0.08660.0958-0.0226-0.01450.22960.03990.178218.2091-25.04917.4372
24.34330.59670.24731.15970.65013.14250.009-0.1377-0.23920.077-0.0049-0.4780.12660.1658-0.02540.1206-0.0208-0.0240.17170.05950.276818.6733-31.854413.6871
33.0561-1.07440.76748.5080.9821.7732-0.1125-0.5009-0.28450.9678-0.01040.92410.273-0.75440.08390.2821-0.10110.0730.53970.07460.21684.7901-26.121525.8649
43.00390.59460.81392.58991.21593.31610.0102-0.29140.19690.06810.03110.0312-0.1973-0.088-0.0450.0835-0.02710.00780.18630.03980.11699.2327-18.803214.2244
53.2350.00870.50292.39940.41211.8242-0.06220.16760.2149-0.27230.10040.0275-0.2261-0.1248-0.01840.167-0.0486-0.00150.24360.08420.13525.2003-19.06642.5943
64.13853.08722.77468.71357.05939.4291-0.01920.1618-0.0008-0.15410.2934-0.4682-0.18420.4941-0.31780.1274-0.04970.0070.20320.04880.165322.806-20.79678.3971
74.7191-1.7821-0.64783.17250.14866.70430.0466-0.368-0.1366-0.078-0.2439-0.5518-0.23060.71270.20670.1909-0.0830.04740.335-0.0080.348928.3343-28.257313.1876
88.8455-2.39545.50148.4890.13893.9540.2479-0.89710.05770.649-0.2238-0.22410.94110.7572-0.0360.3223-0.0466-0.0160.62360.09720.200114.7015-32.72931.875
92.95220.73170.80131.1929-1.83534.4596-0.74690.8359-0.9099-1.28890.15250.25461.6167-2.80360.58260.7089-0.15210.13110.78510.09010.529313.8462-38.696220.8421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:15 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 16:58 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 59:71 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 72:122 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 123:164 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 165:178 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 263:280 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 281:286 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 287:291 )

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