- PDB-2ksq: The myristoylated yeast ARF1 in a GTP and bicelle bound conformation -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2ksq
Title
The myristoylated yeast ARF1 in a GTP and bicelle bound conformation
Components
ADP-ribosylation factor 1
Keywords
TRANSPORT 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
Synthesis of PIPs at the plasma membrane / 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 ...Synthesis of PIPs at the plasma membrane / 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
A 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
Experiment
Method: 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-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D HNCA
1
2
1
3D HN(CA)CB
1
3
1
3DHN(CO)CA
1
4
2
3D C-excited C-CmHm TOCSY
1
5
2
3D NOESY-CH-HMQC
1
6
2
3D NOESY-NH-TROSY
1
7
3
3D NOESY-aromCH-CT-TROSY
1
8
3
3D (H)CCH-TOCSY
1
9
3
3D NOESY-NH-TROSY
1
10
4
3D NOESY-NH-TROSY
1
11
1
2D HSQC-TROSY
1
12
1
2D Jmod-NC'
1
13
1
2D Jmod-NH
1
14
5
2D 1H-15N fast HSQC
1
15
5
2D 1H-R1 HSQC
1
16
3
2D arom-CT-TROSY 1H IPAP
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.8 mM [U-13C; U-15N; U-2H] protein, 95% H2O/5% D2O
95% H2O/5% D2O
2
0.8 mM [VI(d1)L-methyl-1H,13C; U-15N; U-2H] protein, 95% H2O/5% D2O
95% H2O/5% D2O
3
0.8 mM [PHE-1H,13C; U-15N; U-2H] protein, 95% H2O/5% D2O
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