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- PDB-2bao: Solution NMR structure of the myristoylated N-terminal fragment o... -

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Basic information

Entry
Database: PDB / ID: 2bao
TitleSolution NMR structure of the myristoylated N-terminal fragment of Arf6
ComponentsADP-ribosylation factor 6
KeywordsSIGNALING PROTEIN / Myristoyl / N-terminal / Arf6
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / regulation of filopodium assembly / positive regulation of focal adhesion disassembly / MET receptor recycling / endocytic recycling / thioesterase binding / Flemming body / filopodium membrane / TBC/RABGAPs / protein localization to cell surface / cortical actin cytoskeleton organization / hepatocyte apoptotic process / positive regulation of actin filament polymerization / cleavage furrow / endocytic vesicle / synaptic vesicle endocytosis / regulation of presynapse assembly / vesicle-mediated transport / ruffle / signaling adaptor activity / small monomeric GTPase / positive regulation of protein secretion / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / liver development / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / recycling endosome membrane / GDP binding / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / midbody / early endosome membrane / cell cortex / cell differentiation / postsynapse / cell adhesion / endosome / cell division / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor 6 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / ADP-ribosylation factor 6
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsGizachew, D.
CitationJournal: Febs Lett. / Year: 2006
Title: NMR structural studies of the myristoylated N-terminus of ADP ribosylation factor 6 (Arf6).
Authors: Gizachew, D. / Oswald, R.
History
DepositionOct 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2932
Polymers1,0641
Non-polymers2281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ADP-ribosylation factor 6


Mass: 1064.279 Da / Num. of mol.: 1 / Fragment: N-terminal peptide / Source method: obtained synthetically
Details: This sequence is the N-terminal peptide of a protein which occurs naturally in Homo sapiens (human).
References: UniProt: P62330
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 1mM Myristoylated N-terminal Arf6; 5mM acetate buffer
Solvent system: 90% H2O/10% D2O
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: X-PLOR / Version: NIH-2.9.9 / Developer: Lakowski / 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: 50 / Conformers submitted total number: 12

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