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- PDB-3i6x: Crystal structure of the calponin homology domain of IQGAP1 -

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Basic information

Entry
Database: PDB / ID: 3i6x
TitleCrystal structure of the calponin homology domain of IQGAP1
ComponentsRas GTPase-activating-like protein IQGAP1
KeywordsCALMODULIN-BINDING / MEMBRANE PROTEIN / all Helical / Cell membrane / Membrane / Phosphoprotein / PROTEIN BINDING
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 / fibroblast migration / MAP-kinase scaffold activity / 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 / fibroblast migration / MAP-kinase scaffold activity / S100 protein binding / Nephrin family interactions / neuron projection extension / RHOV GTPase cycle / cortical actin cytoskeleton / cellular response to platelet-derived growth factor stimulus / RHOC GTPase cycle / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / lateral plasma membrane / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of protein kinase activity / RHO GTPases activate IQGAPs / fibroblast growth factor receptor signaling pathway / cellular response to epidermal growth factor stimulus / regulation of cytokine production / ruffle / regulation of mitotic cell cycle / RAC1 GTPase cycle / cellular response to calcium ion / protein serine/threonine kinase activator activity / GTPase activator activity / secretory granule membrane / actin filament / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / cytoplasmic side of plasma membrane / small GTPase binding / cytoplasmic ribonucleoprotein granule / 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 / Signaling by BRAF and RAF1 fusions / actin filament binding / cell migration / cell cortex / midbody / growth cone / basolateral plasma membrane / protein phosphatase binding / microtubule / positive regulation of MAPK cascade / molecular adaptor activity / calmodulin binding / ribonucleoprotein complex / cadherin binding / neuron projection / 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 / cytoplasm / cytosol
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / 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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 ...RasGAP protein, C-terminal / RasGAP C-terminus / 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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / WW/rsp5/WWP domain signature. / IQ motif, EF-hand binding site / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKurella, V.B.
CitationJournal: Biochemistry / Year: 2016
Title: The IQGAP1 N-Terminus Forms Dimers, and the Dimer Interface Is Required for Binding F-Actin and Calcium-Bound Calmodulin.
Authors: Liu, J. / Kurella, V.B. / LeCour Jr., L. / Vanagunas, T. / Worthylake, D.K.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 26, 2023Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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

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Assembly

Deposited unit
A: Ras GTPase-activating-like protein IQGAP1
B: Ras GTPase-activating-like protein IQGAP1
C: Ras GTPase-activating-like protein IQGAP1
D: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)89,5504
Polymers89,5504
Non-polymers00
Water68538
1
A: Ras GTPase-activating-like protein IQGAP1
D: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)44,7752
Polymers44,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-13 kcal/mol
Surface area16350 Å2
MethodPISA
2
B: Ras GTPase-activating-like protein IQGAP1
C: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)44,7752
Polymers44,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-12 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.432, 66.421, 83.014
Angle α, β, γ (deg.)99.55, 104.07, 108.69
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22387.439 Da / Num. of mol.: 4
Fragment: N terminal calponin homology domain (UNP residues 1-191)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: IQGAP1, KIAA0051 / Plasmid: pETtrx_1a / Production host: Escherichia coli (E. coli) / References: UniProt: P46940
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M-0.3M Ammonium acetate, 20 % PEG 3350, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9397 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 28, 2009 / Details: Kohzu HLD-4 Double Crystal
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9397 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 36937 / Num. obs: 36983 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 0.09 / Net I/σ(I): 17.47
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3617 / Rsym value: 0.495 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P2X

1p2x


Resolution: 2.5→25 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1858 4.9 %random
Rwork0.234 ---
all-36983 --
obs-36983 98.5 %-
Solvent computationBsol: 30.947 Å2
Displacement parametersBiso max: 122.42 Å2 / Biso mean: 46 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0.46 Å22.95 Å2
2---1.87 Å22.92 Å2
3---1.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 0 38 5374
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3421.5
X-RAY DIFFRACTIONc_scbond_it2.1522
X-RAY DIFFRACTIONc_mcangle_it2.2492
X-RAY DIFFRACTIONc_scangle_it3.3852.5
LS refinement shellHighest resolution: 2.5 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.387 169 -
Rwork0.377 --
obs-3469 97.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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