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- PDB-1u81: Delta-17 Human ADP Ribosylation Factor 1 Complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 1u81
TitleDelta-17 Human ADP Ribosylation Factor 1 Complexed with GDP
ComponentsADP-ribosylation factor 1
KeywordsPROTEIN TRANSPORT / Delta17Arf1 / D17Arf1 / Arf1 / GDP-Binding / Membrane Trafficking / RDC Refinement
Function / homology
Function and homology information


mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / intracellular protein transport / cellular response to virus / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / small GTPase Arf family 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 nucleotide triphosphate hydrolases ...ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / small GTPase Arf family 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Cartesian Min (No RDC), Torsion Angle Min (Ramp RDC), Cartesian Min (Ramp RDC), Cartesian Min (Ro RDC), Torsion Angle Min (RDC)
AuthorsSeidel, R.D. / Amor, J.C. / Kahn, R.A. / Prestegard, J.H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Conformational changes in human Arf1 on nucleotide exchange and deletion of membrane-binding elements.
Authors: Seidel, R.D. / Amor, J.C. / Kahn, R.A. / Prestegard, J.H.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2903
Polymers18,8221
Non-polymers4682
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 11all calculated structures submitted
RepresentativeModel #1all available dipolar data used in calcualtion

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Components

#1: Protein ADP-ribosylation factor 1


Mass: 18822.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Arf1 / Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P84077
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
311Assignment Suite
122IPAP-HSQC
233IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM KPO4, 50mM NaCl, 1mM MgCl2, 5mM NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
27.5% (w/v) etherbicelle in 10mM KPO4, 50mM NaCl, 1mM MgCl2, 90% H2O, 10% D2O90% H2O/10% D2O
34% pentaethylene glycol octylether in 10mM KPO4, 50mM NaCl, 1mM MgCl2, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM salt 7ambient 305 K
250mM salt 7ambient 301 K
350mM salt 7ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA3003

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Processing

NMR softwareName: X-PLOR-NIH / Version: 2.9.1
Developer: C.D.Schwieters, J.J.Kuszewski, N.Tjandra, G.M.Clore
Classification: refinement
RefinementMethod: Cartesian Min (No RDC), Torsion Angle Min (Ramp RDC), Cartesian Min (Ramp RDC), Cartesian Min (Ro RDC), Torsion Angle Min (RDC)
Software ordinal: 1
NMR representativeSelection criteria: all available dipolar data used in calcualtion
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 11 / Conformers submitted total number: 11

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