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- PDB-2rlo: Split PH domain of PI3-kinase enhancer -

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Basic information

Entry
Database: PDB / ID: 2rlo
TitleSplit PH domain of PI3-kinase enhancer
ComponentsCentaurin-gamma 1
KeywordsSIGNALING PROTEIN / Split PH domain / Alternative splicing / ANK repeat / Cytoplasm / GTP-binding / GTPase activation / Metal-binding / Nucleotide-binding / Nucleus / Oncogene / Phosphorylation / Polymorphism / Protein transport / Transport / Zinc / Zinc-finger
Function / homology
Function and homology information


Netrin-1 signaling / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / Flemming body / endosomal transport / protein kinase activator activity / positive regulation of protein kinase activity / GTPase activator activity / negative regulation of protein catabolic process / protein transport ...Netrin-1 signaling / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / Flemming body / endosomal transport / protein kinase activator activity / positive regulation of protein kinase activity / GTPase activator activity / negative regulation of protein catabolic process / protein transport / actin cytoskeleton organization / negative regulation of neuron apoptotic process / endosome / GTPase activity / GTP binding / protein kinase binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / small GTPase Rab1 family profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. ...Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / small GTPase Rab1 family profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWen, W. / Zhang, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Split pleckstrin homology domain-mediated cytoplasmic-nuclear localization of PI3-kinase enhancer GTPase
Authors: Yan, J. / Wen, W. / Chan, L.N. / Zhang, M.
History
DepositionJul 21, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: 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: Centaurin-gamma 1


Theoretical massNumber of molelcules
Total (without water)14,3281
Polymers14,3281
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Centaurin-gamma 1 / ARF-GAP with GTP-binding protein-like / ankyrin repeat and pleckstrin homology domains 2 / AGAP-2 / ...ARF-GAP with GTP-binding protein-like / ankyrin repeat and pleckstrin homology domains 2 / AGAP-2 / Phosphatidylinositol-3-kinase enhancer / PIKE / GTP-binding and GTPase-activating protein 2 / GGAP2


Mass: 14328.110 Da / Num. of mol.: 1 / Fragment: UNP residues 674-752, 846-914, split_PH_domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENTG1, AGAP2, KIAA0167 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99490
Sequence detailsDELETION OF 853-872 IS MISSING IN ISOFORM 2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1222D 1H-1H NOESY
1333D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 15N] split PH domain, 90% H2O/10% D2O90% H2O/10% D2O
21mM split PH domain, 100% D2O100% D2O
31mM [U-100% 13C; U-100% 15N] split PH domain, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMsplit PH domain[U-100% 15N]1
1 mMsplit PH domain2
1 mMsplit PH domain[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges, Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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