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- PDB-2k9a: The Solution Structure of the Arl2 Effector, BART -

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Basic information

Entry
Database: PDB / ID: 2k9a
TitleThe Solution Structure of the Arl2 Effector, BART
ComponentsADP-ribosylation factor-like protein 2-binding protein
KeywordsPROTEIN BINDING / Protein / Effector / small G protein / Alternative splicing / Cytoplasm / Mitochondrion / Phosphoprotein
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / GTPase regulator activity / maintenance of protein location in nucleus / positive regulation of tyrosine phosphorylation of STAT protein / mitochondrial intermembrane space / cilium / spindle / midbody / transcription coactivator activity / mitochondrial matrix ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / GTPase regulator activity / maintenance of protein location in nucleus / positive regulation of tyrosine phosphorylation of STAT protein / mitochondrial intermembrane space / cilium / spindle / midbody / transcription coactivator activity / mitochondrial matrix / centrosome / signal transduction / nucleoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor-like protein 2-binding protein / Adp-ribosylation factor-like protein 2-binding protein fold / ADP-ribosylation factor-like 2-binding protein, domain / BART domain / BART domain superfamily / The ARF-like 2 binding protein BART / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor-like protein 2-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
AuthorsBailey, L.K. / Campbell, L.J. / Evetts, K.A. / Littlefield, K. / Rajendra, E. / Nietlispach, D. / Owen, D. / Mott, H.R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Structure of Binder of Arl2 (BART) Reveals a Novel G Protein Binding Domain: IMPLICATIONS FOR FUNCTION.
Authors: Bailey, L.K. / Campbell, L.J. / Evetts, K.A. / Littlefield, K. / Rajendra, E. / Nietlispach, D. / Owen, D. / Mott, H.R.
History
DepositionOct 6, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: 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_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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 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: ADP-ribosylation factor-like protein 2-binding protein


Theoretical massNumber of molelcules
Total (without water)16,1631
Polymers16,1631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein ADP-ribosylation factor-like protein 2-binding protein / ARF-like 2-binding protein / Binder of ARF2 protein 1


Mass: 16162.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL2BP, BART, BART1 / Plasmid: pET 16b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2Y0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1423D HNCA
1523D HN(CO)CA
1623D HN(CA)CB
1723D HN(COCA)CB
1823D 1H-13C NOESY
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity[U-100% 15N]1
10 %D2O1
50 mMsodium phosphate1
150 mMsodium chloride1
0.05 %sodium azide1
1 mMentity[U-100% 13C; U-100% 15N]2
10 %D2O2
50 mMsodium phosphate2
150 mMsodium chloride2
0.05 %sodium azide2
Sample conditionsIonic strength: 20 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, J. et al.structure solution
CNSBrunger, A.T. et al.refinement
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNchemical shift calculation
CcpNmr AnalysisCCPNpeak picking
AzaraBoucher, W. et al.processing
TALOSCornilescu, G. et al.torsion angle prediction
TENSOR2Dosset, P. et al.model free analysis
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 50

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