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- PDB-1v61: Solution Structure of the Pleckstrin Homology Domain of alpha-Pix -

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Basic information

Entry
Database: PDB / ID: 1v61
TitleSolution Structure of the Pleckstrin Homology Domain of alpha-Pix
ComponentsRac/Cdc42 guanine nucleotide exchange factor (GEF) 6
KeywordsSIGNALING PROTEIN / Pleckstrin homology domain / Guanine nucleotide exchange factor / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / : / G beta:gamma signalling through CDC42 / NRAGE signals death through JNK / G alpha (12/13) signalling events / lamellipodium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / lamellipodium / intracellular signal transduction
Similarity search - Function
Rho guanine nucleotide exchange factor 6, SH3 domain / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Smooth muscle protein/calponin / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain ...Rho guanine nucleotide exchange factor 6, SH3 domain / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Smooth muscle protein/calponin / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
: / Rho guanine nucleotide exchange factor 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNakanishi, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the Pleckstrin Homology Domain of alpha-Pix
Authors: Nakanishi, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionNov 26, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6


Theoretical massNumber of molelcules
Total (without water)14,6271
Polymers14,6271
Non-polymers00
Water0
1


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

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Components

#1: Protein Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 / PAK-interacting exchange factor alpha


Mass: 14626.534 Da / Num. of mol.: 1 / Fragment: Pleckstrin homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1700038J06 / Plasmid: P030212-43 / References: GenBank: 22266730, UniProt: Q8K4I3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.15mM PH domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.87Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.structure solution
CYANA1.0.7Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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