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- PDB-2ksq: The myristoylated yeast ARF1 in a GTP and bicelle bound conformation -

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Basic information

Entry
Database: PDB / ID: 2ksq
TitleThe myristoylated yeast ARF1 in a GTP and bicelle bound conformation
ComponentsADP-ribosylation factor 1ARF1
KeywordsTRANSPORT PROTEIN / ARF / myristoylated / myristoyl / GTP / bicelle / ER-Golgi transport / Golgi apparatus / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Protein transport / Transport
Function / homology
Function and homology information


VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Golgi vesicle transport / Golgi to plasma membrane transport / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport ...VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Golgi vesicle transport / Golgi to plasma membrane transport / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / small monomeric GTPase / macroautophagy / intracellular protein transport / GTPase activity / GTP binding / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / 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 / P-loop containing nucleoside triphosphate hydrolase ...ADP-ribosylation factor 1-5 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Chem-MTN / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 4
AuthorsLiu, Y. / Kahn, R. / Prestegard, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Dynamic structure of membrane-anchored Arf*GTP.
Authors: Liu, Y. / Kahn, R.A. / Prestegard, J.H.
History
DepositionJan 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Non-polymer description

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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)22,3617
Polymers20,5161
Non-polymers1,8456
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 / 280structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ADP-ribosylation factor 1 / ARF1


Mass: 20515.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARF1, YDL192W, D1244 / Production host: Escherichia coli (E. coli) / References: UniProt: P11076
#2: Chemical
ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
Sequence detailsA MYRISTOYL GROUP (DERIVED FROM MYRISTIC ACID) IS COVALENTLY ATTACHED TO THE N-TERMINUS VIA AN ...A MYRISTOYL GROUP (DERIVED FROM MYRISTIC ACID) IS COVALENTLY ATTACHED TO THE N-TERMINUS VIA AN AMIDE BOND. FURTHERMORE, WILD-TYPE PROTEIN WAS USED FOR ALL EXPERIMENTS (NOESY AND RDC) EXCEPT FOR THE PRE EXPERIMENTS WHICH REQUIRES A X-TO-CYS MUTATION. THE CYS MUTATIONS ARE NOT SIMULTANEOUSLY PRESENT BUT ONE AT A TIME. HOWEVER THE PRE DATA WERE COMBINED DURING CALCULATION AND THEREFORE IT APPEARS ALL THESE RESIDUES ARE REPLACED BY CYS IN THE FINAL PDB.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: T55, K59, R83, R117, and S176 are mutated one at a time to cysteine for PRE measurement. Therefore these residues are replaced by "3M" (cys-mtsl) in the primary sequence
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CA)CB
1313D HN(CO)CA
1423D C-excited C-CmHm TOCSY
1523D NOESY-CH-HMQC
1623D NOESY-NH-TROSY
1733D NOESY-aromCH-CT-TROSY
1833D (H)CCH-TOCSY
1933D NOESY-NH-TROSY
11043D NOESY-NH-TROSY
11112D HSQC-TROSY
11212D Jmod-NC'
11312D Jmod-NH
11452D 1H-15N fast HSQC
11552D 1H-R1 HSQC
11632D arom-CT-TROSY 1H IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-13C; U-15N; U-2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [VI(d1)L-methyl-1H,13C; U-15N; U-2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
30.8 mM [PHE-1H,13C; U-15N; U-2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
40.8 mM [U-100% 13C; U-100% 15N; U-70% 2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
50.3 mM [U-15N; 70%-2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1-1[U-13C; U-15N; U-2H]1
0.8 mMentity_1-2[VI(d1)L-methyl-1H,13C; U-15N; U-2H]2
0.8 mMentity_1-3[PHE-1H,13C; U-15N; U-2H]3
0.8 mMentity_1-4[U-100% 13C; U-100% 15N; U-70% 2H]4
0.3 mMentity_1-5[U-15N; 70%-2H]5
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameDeveloperClassification
VNMRJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddarddata analysis
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 280 / Conformers submitted total number: 20

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