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- PDB-3fay: Crystal structure of the GAP-related domain of IQGAP1 -

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Basic information

Entry
Database: PDB / ID: 3fay
TitleCrystal structure of the GAP-related domain of IQGAP1
ComponentsRas GTPase-activating-like protein IQGAP1
KeywordsMEMBRANE PROTEIN / ALL ALPHA / Calmodulin-binding / Cell membrane / Membrane / Phosphoprotein
Function / homology
Function and homology information


negative regulation of dephosphorylation / mitotic actomyosin contractile ring assembly actin filament organization / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions / neuron projection extension ...negative regulation of dephosphorylation / mitotic actomyosin contractile ring assembly actin filament organization / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions / neuron projection extension / RHOV GTPase cycle / cortical actin cytoskeleton / RHOC GTPase cycle / cellular response to platelet-derived growth factor stimulus / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / CDC42 GTPase cycle / lateral plasma membrane / RHOA GTPase cycle / positive regulation of protein kinase activity / RAC2 GTPase cycle / fibroblast growth factor receptor signaling pathway / RHO GTPases activate IQGAPs / ruffle / regulation of mitotic cell cycle / regulation of cytokine production / cellular response to epidermal growth factor stimulus / RAC1 GTPase cycle / cellular response to calcium ion / GTPase activator activity / protein serine/threonine kinase activator activity / secretory granule membrane / actin filament / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / small GTPase binding / cytoplasmic ribonucleoprotein granule / cytoplasmic side of plasma membrane / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / Signaling by BRAF and RAF1 fusions / cell migration / cell cortex / growth cone / midbody / basolateral plasma membrane / protein phosphatase binding / microtubule / positive regulation of MAPK cascade / molecular adaptor activity / calmodulin binding / neuron projection / cadherin binding / ribonucleoprotein complex / apical plasma membrane / protein domain specific binding / axon / focal adhesion / calcium ion binding / Neutrophil degranulation / protein kinase binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain ...RasGAP protein, C-terminal / RasGAP C-terminus / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ras GTPase-activating-like protein IQGAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKurella, V.B. / Richard, J.M. / Parke, C.L. / Bellamy, H. / Worthylake, D.K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of the GTPase-activating protein-related domain from IQGAP1.
Authors: Kurella, V.B. / Richard, J.M. / Parke, C.L. / Lecour, L.F. / Bellamy, H.D. / Worthylake, D.K.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras GTPase-activating-like protein IQGAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6572
Polymers44,5351
Non-polymers1221
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.133, 42.115, 59.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ras GTPase-activating-like protein IQGAP1 / p195


Mass: 44535.023 Da / Num. of mol.: 1 / Fragment: GAP-related domain (GRD)
Source method: isolated from a genetically manipulated source
Details: ligation independent cloning vector / Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP1, KIAA0051 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: P46940
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG 2000 methyl ether, 500mM MgCl2, 100mM Tris HCL, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.97924, 0.97900, 0.92523
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.9791
30.925231
ReflectionResolution: 2.2→25 Å / Num. all: 20692 / Num. obs: 20692 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.062 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.242 / % possible all: 38.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→25 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS default
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 1971 -random
Rwork0.2284 ---
obs-19520 86.8 %-
Displacement parametersBiso mean: 47.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 8 147 3192

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