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- PDB-2dfk: Crystal structure of the CDC42-Collybistin II complex -

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Basic information

Entry
Database: PDB / ID: 2dfk
TitleCrystal structure of the CDC42-Collybistin II complex
Components
  • cell division cycle 42 isoform 1
  • collybistin II
KeywordsCELL CYCLE / DH domain / PH domain
Function / homology
Function and homology information


CDC42 GTPase cycle / GABA receptor activation / NRAGE signals death through JNK / regulation of postsynaptic specialization assembly / G alpha (12/13) signalling events / RHOQ GTPase cycle / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex ...CDC42 GTPase cycle / GABA receptor activation / NRAGE signals death through JNK / regulation of postsynaptic specialization assembly / G alpha (12/13) signalling events / RHOQ GTPase cycle / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / postsynaptic specialization / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / 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 / GTP-dependent protein binding / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / positive regulation of intracellular protein transport / neuropilin signaling pathway / cell junction assembly / filopodium assembly / glycinergic synapse / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / thioesterase binding / embryonic heart tube development / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / DCC mediated attractive signaling / sprouting angiogenesis / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / phagocytosis, engulfment / establishment or maintenance of cell polarity / heart contraction / Myogenesis / receptor clustering / RHOJ GTPase cycle / Golgi organization / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / GABA-ergic synapse / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / RAC1 GTPase cycle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / positive regulation of DNA replication / secretory granule / guanyl-nucleotide exchange factor activity / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse
Similarity search - Function
Rho guanine nucleotide exchange factor 9, SH3 domain / Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / SOS1/NGEF-like PH domain / Variant SH3 domain / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain ...Rho guanine nucleotide exchange factor 9, SH3 domain / Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / SOS1/NGEF-like PH domain / Variant SH3 domain / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog / Rho guanine nucleotide exchange factor 9
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsXiang, S. / Kim, E.Y. / Connelly, J.J. / Nassar, N. / Kirsch, J. / Winking, J. / Schwarz, G. / Schindelin, H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of Cdc42 in Complex with Collybistin II, a Gephyrin-interacting Guanine Nucleotide Exchange Factor.
Authors: Xiang, S. / Kim, E.Y. / Connelly, J.J. / Nassar, N. / Kirsch, J. / Winking, J. / Schwarz, G. / Schindelin, H.
History
DepositionMar 2, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: collybistin II
B: cell division cycle 42 isoform 1
C: collybistin II
D: cell division cycle 42 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,38612
Polymers139,6424
Non-polymers7458
Water10,467581
1
A: collybistin II
B: cell division cycle 42 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2857
Polymers69,8212
Non-polymers4645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-40 kcal/mol
Surface area29180 Å2
MethodPISA
2
C: collybistin II
D: cell division cycle 42 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1015
Polymers69,8212
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-37 kcal/mol
Surface area27060 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-88 kcal/mol
Surface area53250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.957, 147.499, 167.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein collybistin II


Mass: 48254.941 Da / Num. of mol.: 2 / Fragment: residues 10-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PTYB12 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9QX73
#2: Protein cell division cycle 42 isoform 1 / GTP-binding protein / 25KD / CDC42


Mass: 21565.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P60953
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Potassium dihydrogen phosphate, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 72590 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.075 / Net I/σ(I): 22.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.52 / % possible all: 83.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOE

1foe


Resolution: 2.15→47.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.593 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3782 5 %RANDOM
Rwork0.18 ---
obs0.183 72076 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9002 0 46 581 9629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229247
X-RAY DIFFRACTIONr_bond_other_d0.0030.028336
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.95712448
X-RAY DIFFRACTIONr_angle_other_deg0.981319465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63151088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210114
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021897
X-RAY DIFFRACTIONr_nbd_refined0.2310.22029
X-RAY DIFFRACTIONr_nbd_other0.240.29566
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.25644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2440
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.55460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04928850
X-RAY DIFFRACTIONr_scbond_it3.32633787
X-RAY DIFFRACTIONr_scangle_it5.524.53598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 224
Rwork0.21 4417
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)
10.6897-0.01850.18671.67480.56391.34540.06670.0205-0.07-0.0065-0.05980.0363-0.1129-0.0004-0.00690.20390.011-0.01180.2419-0.00870.263940.820211.529720.8668
24.0656-0.50021.50463.8265-0.98895.4229-0.006-0.4153-0.26850.10840.19040.30770.2125-0.4546-0.18440.27380.14740.02140.24510.14730.120123.775322.6372-13.4878
30.6118-0.06180.10712.39470.47321.58950.04140.0909-0.0537-0.2885-0.0391-0.3384-0.0120.2851-0.00230.20890.03610.06620.28820.0020.29154.0935-0.15616.3448
40.8634-0.52370.40921.3443-0.51830.8136-0.0268-0.05160.01520.01770.0746-0.0451-0.02220.0392-0.04780.222-0.0257-0.00690.25440.04230.277848.7864-33.63336.9794
51.1471-0.0751-0.17651.7504-1.2235.58460.02570.1462-0.1767-0.18260.0022-0.08120.5534-0.0768-0.0280.2633-0.00580.01690.2459-0.04080.225547.339-37.7865-2.6298
61.61390.2304-0.0380.9730.10071.67390.02210.02640.04550.0174-0.06110.1028-0.0453-0.13640.0390.2305-0.01520.01320.2220.01710.267225.5993-38.672140.5404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA43 - 24634 - 237
2X-RAY DIFFRACTION2AA247 - 401238 - 392
3X-RAY DIFFRACTION3BB1 - 1914 - 194
4X-RAY DIFFRACTION4CC51 - 24642 - 237
5X-RAY DIFFRACTION5CC247 - 397238 - 388
6X-RAY DIFFRACTION6DD-2 - 1911 - 194

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