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- PDB-2kg5: NMR Solution structure of ARAP3-SAM -

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Basic information

Entry
Database: PDB / ID: 2kg5
TitleNMR Solution structure of ARAP3-SAM
ComponentsArf-GAP, Rho-GAP domain, ANK repeat and PH domain-containing protein 3
KeywordsSIGNALING PROTEIN / SAM DOMAIN / HELIX BUNDLE / Cell membrane / Cell projection / Cytoplasm / Cytoskeleton / GTPase activation / Membrane / Metal-binding / Phosphoprotein / Polymorphism / Zinc / Zinc-finger
Function / homology
Function and homology information


phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / cytoskeleton organization / vesicle-mediated transport / ruffle / RAC1 GTPase cycle / lamellipodium ...phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / cytoskeleton organization / vesicle-mediated transport / ruffle / RAC1 GTPase cycle / lamellipodium / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
ARAP, RhoGAP domain / 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 / Transcription Factor, Ets-1 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain ...ARAP, RhoGAP domain / 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 / Transcription Factor, Ets-1 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / DNA polymerase; domain 1 / PH-like domain superfamily / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsLeone, M. / Pellecchia, M.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam.
Authors: Leone, M. / Cellitti, J. / Pellecchia, M.
History
DepositionMar 5, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arf-GAP, Rho-GAP domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)10,8641
Polymers10,8641
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Arf-GAP, Rho-GAP domain, ANK repeat and PH domain-containing protein 3 / Centaurin-delta-3 / Cnt-d3


Mass: 10864.156 Da / Num. of mol.: 1 / Fragment: SAM Domain, residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARAP3, CENTD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWN8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1223D 1H-15N NOESY
1333D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 100% D2O100% D2O
21 mM [U-100% 15N] protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-100% 13C; U-100% 15N] protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity1
2.7 mMpotassium chloride1
137 mMsodium chloride1
11.9 mMphosphates1
0.3 %sodium azide1
1 mMentity[U-100% 15N]2
2.7 mMpotassium chloride2
137 mMsodium chloride2
11.9 mMphosphates2
0.3 %sodium azide2
1 mMentity[U-100% 13C; U-100% 15N]3
2.7 mMpotassium chloride3
137 mMsodium chloride3
11.9 mMphosphates3
0.3 %sodium azide3
Sample conditionspH: 7.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin2.1Bruker Biospinprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: The structures were generated by only using CYANA
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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