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- PDB-2rr8: Solution structure of calponin homology domain of IQGAP1 -

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Basic information

Entry
Database: PDB / ID: 2rr8
TitleSolution structure of calponin homology domain of IQGAP1
ComponentsIQGAP1 protein
KeywordsPROTEIN BINDING / F-actin binding protein
Function / homology
Function and homology information


negative regulation of dephosphorylation / plasma membrane bounded cell projection / 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 ...negative regulation of dephosphorylation / plasma membrane bounded cell projection / 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 / RHOQ GTPase cycle / cellular response to platelet-derived growth factor stimulus / phosphatidylinositol-3,4,5-trisphosphate binding / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / CDC42 GTPase cycle / lateral plasma membrane / fibroblast growth factor receptor signaling pathway / RHOA GTPase cycle / positive regulation of protein kinase activity / RAC2 GTPase cycle / 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 side of plasma membrane / 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 / 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 / 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. / 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 / IQGAP1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsUmemoto, R. / Nishida, N. / Ogino, S. / Shimada, I.
CitationJournal: J.Biomol.Nmr / Year: 2010
Title: NMR structure of the calponin homology domain of human IQGAP1 and its implications for the actin recognition mode.
Authors: Umemoto, R. / Nishida, N. / Ogino, S. / Shimada, I.
History
DepositionJun 9, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IQGAP1 protein


Theoretical massNumber of molelcules
Total (without water)22,0321
Polymers22,0321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein IQGAP1 protein


Mass: 22032.256 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6P1N4, UniProt: P46940*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCA
1613D HN(CA)CB
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1923D 1H-13C NOESY
11013D 1H-15N NOESY
11133D HNHA
11213D H(CCO)NH
11313D HN(CO)CA
11413D HBHA(CO)NH
11513D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.90 mM [U-99% 13C; U-99% 15N] CH domain-1, 20 mM sodium phosphate-2, 150 mM sodium chloride-3, 1 mM DTT-4, 1 mM sodium azide-5, 90% H2O/10% D2O90% H2O/10% D2O
20.90 mM [U-99% 13C; U-99% 15N] CH domain-6, 20 mM sodium phosphate-7, 150 mM sodium chloride-8, 1 mM DTT-9, 1 mM sodium azide-10, 100% D2O100% D2O
30.90 mM [U-99% 15N] CH domain-11, 20 mM sodium phosphate-12, 150 mM sodium chloride-13, 1 mM DTT-14, 1 mM sodium azide-15, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.90 mMCH domain-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMDTT-41
1 mMsodium azide-51
0.90 mMCH domain-6[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-72
150 mMsodium chloride-82
1 mMDTT-92
1 mMsodium azide-102
0.90 mMCH domain-11[U-99% 15N]3
20 mMsodium phosphate-123
150 mMsodium chloride-133
1 mMDTT-143
1 mMsodium azide-153
Sample conditionsIonic strength: 0.17 / pH: 7.4 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler, Wuthrich / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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