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- PDB-5frg: The NMR Structure of the Cdc42-interacting region of TOCA1 -

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Basic information

Entry
Database: PDB / ID: 5frg
TitleThe NMR Structure of the Cdc42-interacting region of TOCA1
ComponentsFORMIN-BINDING PROTEIN 1-LIKE
KeywordsPROTEIN BINDING / FORMIN-BINDING PROTEIN LIKE-1 / LIPID-BINDING / CDC42 / CYTOSKELETON / ENDOCYTOSIS / HR1 / REM / MEMBRANE / PLASMA MEMBRANE / RHO FAMILY / SMALL G PROTEINS
Function / homology
Function and homology information


Clathrin-mediated endocytosis / autophagy / endocytosis / cell cortex / cytoplasmic vesicle / cytoskeleton / lipid binding / signal transduction / plasma membrane
Similarity search - Function
Formin-binding protein 1-like / FNBP1L, SH3 domain / FNBP1L, F-BAR domain / HR1 rho-binding domain / REM-1 domain profile. / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. ...Formin-binding protein 1-like / FNBP1L, SH3 domain / FNBP1L, F-BAR domain / HR1 rho-binding domain / REM-1 domain profile. / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Formin-binding protein 1-like
Similarity search - Component
Biological speciesXENOPUS TROPICALIS
MethodSOLUTION NMR / ARIA2.3; CNS 1.2
AuthorsWatson, J.R. / Nietlispach, D. / Owen, D. / Mott, H.R.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Investigation of the Interaction between Cdc42 and its Effector Toca1: Handover of Cdc42 to the Actin Regulator N-Wasp is Facilitated by Differential Binding Affinities.
Authors: Watson, J.R. / Fox, H.M. / Nietlispach, D. / Gallop, J.L. / Owen, D. / Mott, H.R.
History
DepositionDec 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 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 2.2Jun 19, 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: FORMIN-BINDING PROTEIN 1-LIKE


Theoretical massNumber of molelcules
Total (without water)12,1121
Polymers12,1121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein FORMIN-BINDING PROTEIN 1-LIKE / TOCA1 / TRANSDUCER OF CDC42-DEPENDENT ACTIN ASSEMBLY PROTEIN 1 / TOCA-1


Mass: 12111.687 Da / Num. of mol.: 1 / Fragment: HOMOLOGY REGION 1, UNP RESIDUES 330-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog)
Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6GUF4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115NHSQC
221HN(CO)CA
331HN(CO)CACB
441HNCA
551HN(CA)CB
661HNCO
77115NHSQCNOESY
881NOESY13CHSQC
991HCCHTOCSY
1010113CHSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N TOCA1 HR1 DOMAIN

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.157.41.0 atm298.0 K
20.157.41.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3; CNS1.2CNS1.2W.RIEPING,M.HABECK,B.BARDIAUX,A.BERNARD,T.E. MALLIAVIN,M.NILGES; A.T.BRUNGER,P.D.ADAMS,G.M.CLORE, W.L.DELANO,P.GROS,R.W.GROSSE-KUNSTLEVE,J.S.JIANG, J.KUSZEWSKI,M.NILGES,N.S.PANNU,R.J.READ,L.M.RICE, T.SIMONSON,G.L.WARREN.refinement
ARIA2.3structure solution
CcpNmr Analysis2.3structure solution
Azarastructure solution
CNS1.2structure solution
RefinementMethod: ARIA2.3; CNS 1.2 / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 35

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