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- PDB-1grn: CRYSTAL STRUCTURE OF THE CDC42/CDC42GAP/ALF3 COMPLEX. -

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Basic information

Entry
Database: PDB / ID: 1grn
TitleCRYSTAL STRUCTURE OF THE CDC42/CDC42GAP/ALF3 COMPLEX.
Components
  • PROTEIN (GTP BINDING PROTEIN)
  • PROTEIN (RHO GTPASE ACTIVATING PROTEIN)
KeywordsGENE REGULATION / TRANSITION-STATE / G-PROTEIN / CDC42 / GAP / ALF3
Function / homology
Function and homology information


negative regulation of endocytic recycling / 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 ...negative regulation of endocytic recycling / 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 / transferrin transport / 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 / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of postsynapse organization / RND2 GTPase cycle / positive regulation of filopodium assembly / endosomal transport / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / RHOB GTPase cycle / small GTPase-mediated signal transduction / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / macrophage differentiation / RHOG GTPase cycle / RHOA 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 / 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 / GTPase activator activity / 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
Similarity search - Function
: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Cdc42 / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain ...: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Cdc42 / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Small GTPase Rho / small GTPase Rho family profile. / Rho GTPase activation protein / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Cell division control protein 42 homolog / Rho GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsNassar, N. / Hoffman, G.R. / Clardy, J.C. / Cerione, R.A.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP.
Authors: Nassar, N. / Hoffman, G.R. / Manor, D. / Clardy, J.C. / Cerione, R.A.
History
DepositionJul 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GTP BINDING PROTEIN)
B: PROTEIN (RHO GTPASE ACTIVATING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8795
Polymers44,3282
Non-polymers5513
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-28 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 69.000, 129.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein PROTEIN (GTP BINDING PROTEIN)


Mass: 21283.582 Da / Num. of mol.: 1 / Fragment: CDC42
Source method: isolated from a genetically manipulated source
Details: GDP, MG++, ALF3 / Source: (gene. exp.) Homo sapiens (human)
Description: PROTEINS EXPRESSED IN ESCHERICHIA COLI AS HIS-TAGGED FUSION PROTEINS.;
Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#2: Protein PROTEIN (RHO GTPASE ACTIVATING PROTEIN)


Mass: 23044.260 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN OF CDC42GAP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: PROTEINS EXPRESSED IN ESCHERICHIA COLI AS HIS-TAGGED FUSION PROTEINS.
Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960

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Non-polymers , 4 types, 75 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.64 Å3/Da / Density % sol: 49 %
Description: THE STRUCTURE WAS SOLVED BY A COMBINATION OF MAD PHASING AND MOLECULAR REPLACEMENT.
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 %(w/v)PEG40001reservoir
20.2 Mmagnesium acetate1reservoir
30.10 mM1reservoirAlCl3
410-30 mM1reservoirNaF

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.92
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 23543 / % possible obs: 85.9 % / Redundancy: 5.6 % / Rsym value: 0.064 / Net I/σ(I): 29
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 9.3 / Rsym value: 0.331 / % possible all: 85.9
Reflection
*PLUS
Num. measured all: 129060 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
CCP4model building
X-PLOR3.851refinement
XDSdata reduction
CCP4phasing
RefinementMethod to determine structure: MAD
Starting model: CDC42 IN THE GTP FORM

Resolution: 2.1→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE AL AND F ATOMS WERE RESTRAINED TO BE PLANAR.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1765 10 %RANDOM
Rwork0.211 ---
obs0.211 18794 85.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 33 72 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.173
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.57
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.162
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.7151.5
X-RAY DIFFRACTIONx_mcangle_it3.3292
X-RAY DIFFRACTIONx_scbond_it3.8272
X-RAY DIFFRACTIONx_scangle_it4.5782.5
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3094 136 10 %
Rwork0.2785 1069 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2GDP.PARGDP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.57
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.162
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % reflection Rfree: 10 %

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