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- PDB-5l0o: IQGAP1 calponin homology domain fragment (CHDF) mutant K161C unde... -

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Basic information

Entry
Database: PDB / ID: 5l0o
TitleIQGAP1 calponin homology domain fragment (CHDF) mutant K161C under oxidizing conditions
ComponentsRas GTPase-activating-like protein IQGAP1
KeywordsSIGNALING PROTEIN / Calponin homology / disulfide-bonded dimer
Function / homology
Function and homology information


mitotic actomyosin contractile ring assembly actin filament organization / negative regulation of dephosphorylation / caveola assembly / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions ...mitotic actomyosin contractile ring assembly actin filament organization / negative regulation of dephosphorylation / caveola assembly / 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 / RHOQ GTPase cycle / platelet-derived growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate binding / RHOU GTPase cycle / CDC42 GTPase cycle / lateral plasma membrane / fibroblast growth factor receptor signaling pathway / RHOA GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / cellular response to platelet-derived growth factor stimulus / ruffle / RAC1 GTPase cycle / regulation of cytokine production / cellular response to calcium ion / regulation of mitotic cell cycle / GTPase activator activity / cellular response to epidermal growth factor stimulus / secretory granule membrane / protein serine/threonine kinase activator activity / actin filament / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / small GTPase binding / cytoplasmic side of plasma membrane / epidermal growth factor receptor signaling pathway / cytoplasmic ribonucleoprotein granule / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cell migration / growth cone / midbody / cell cortex / protein phosphatase binding / basolateral plasma membrane / molecular adaptor activity / microtubule / calmodulin binding / positive regulation of MAPK cascade / neuron projection / apical plasma membrane / cadherin binding / ribonucleoprotein complex / 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 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain 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 (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain 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 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / 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 / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLiu, J. / Worthylake, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084072 United States
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, L. / Vanagunas, T. / Worthylake, D.K.
History
DepositionJul 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 30, 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
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)89,4464
Polymers89,4464
Non-polymers00
Water00
1
A: Ras GTPase-activating-like protein IQGAP1
B: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)44,7232
Polymers44,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-13 kcal/mol
Surface area16640 Å2
MethodPISA
2
C: Ras GTPase-activating-like protein IQGAP1
D: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)44,7232
Polymers44,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.752, 72.464, 73.272
Angle α, β, γ (deg.)77.15, 72.07, 86.80
Int Tables number1
Space group name H-MP1
DetailsDimer according to gel filtration, mutagenesis, shape complementary analysis

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Components

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


Mass: 22361.402 Da / Num. of mol.: 4 / Mutation: K161C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP1, KIAA0051 / Production host: Escherichia coli (E. coli)
Strain (production host): in Rosetta Gami 2(DE3) pLysS cells (EMD4Biosciences)
References: UniProt: P46940
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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 18% PEG 3350, 10% ethylene glycol, 10% glucose, 100mM -160mM potassium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→68.06 Å / Num. obs: 41528 / % possible obs: 98.4 % / Redundancy: 3.13 % / Rmerge(I) obs: 0.0847 / Net I/σ(I): 25.57
Reflection shellResolution: 2.36→2.46 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.3504 / Mean I/σ(I) obs: 2.14 / % possible all: 94.8

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Processing

Software
NameClassification
CNSrefinement
SAINTdata reduction
XPREPdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I6X

3i6x


Resolution: 2.36→15 Å / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2056 4.9 %RANDOM
Rwork0.262 ---
obs0.262 38960 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.36→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 0 0 5436

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