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- PDB-2ke4: The NMR structure of the TC10 and Cdc42 interacting domain of CIP4 -

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Basic information

Entry
Database: PDB / ID: 2ke4
TitleThe NMR structure of the TC10 and Cdc42 interacting domain of CIP4
ComponentsCdc42-interacting protein 4
KeywordsMEMBRANE PROTEIN / CIP4 / Cdc42 / TC10 / coiled-coil / Alternative splicing / Cell membrane / Coiled coil / Cytoplasm / Cytoskeleton / Endocytosis / Golgi apparatus / Lipid-binding / Lysosome / Membrane / Phosphoprotein / SH3 domain
Function / homology
Function and homology information


cell communication / RHOQ GTPase cycle / phagocytic cup / cell projection / endocytosis / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / lysosome / cytoskeleton ...cell communication / RHOQ GTPase cycle / phagocytic cup / cell projection / endocytosis / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / lysosome / cytoskeleton / intracellular membrane-bounded organelle / lipid binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #470 / Fes/CIP4, and EFC/F-BAR homology domain / HR1 rho-binding domain / REM-1 domain profile. / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Helix Hairpins ...Helix Hairpins - #470 / Fes/CIP4, and EFC/F-BAR homology domain / HR1 rho-binding domain / REM-1 domain profile. / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Helix Hairpins / SH3 domain / Helix non-globular / Special / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Cdc42-interacting protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKumeta, H. / Kanoh, D. / Kobashigawa, Y. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2009
Title: The NMR structure of the TC10- and Cdc42-interacting domain of CIP4.
Authors: Kobashigawa, Y. / Kumeta, H. / Kanoh, D. / Inagaki, F.
History
DepositionJan 22, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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: Cdc42-interacting protein 4


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cdc42-interacting protein 4 / Thyroid receptor-interacting protein 10 / TRIP-10 / Protein Felic / Salt tolerant protein / hSTP


Mass: 11533.915 Da / Num. of mol.: 1 / Fragment: residues 328-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP10, CIP4, STOT, STP / Production host: Escherichia coli (E. coli) / References: UniProt: Q15642

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CO)CA
1513D HNCA
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HN(CA)HA
1913D HBHA(CO)NH
11013D C(CO)NH
11113D H(CCO)NH
11213D (H)CCH-TOCSY
11313D 1H-15N NOESY
11413D 1H-13C NOESY
11512D (HB)CB(CGCD)HD
11612D (HB)CB(CGCDCE)HE
11713D 1H-13C NOESY aromatic
11813D (H)CCH-TOCSY (Aromatic)
11912D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 20 mM MES-1, 150 mM sodium chloride-2, 1 mM DTT-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMMES-11
150 mMsodium chloride-21
1 mMDTT-31
Sample conditionsIonic strength: 0.15 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
Sparky3.11Goddardrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing, 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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