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2bau

Solution NMR structure of the micelle-bound myristoylated N-terminal Arf6

Method: SOLUTION NMR Dmax: 11.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-ribosylation factor 6

OrganismNot specified

UniProt P62330

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–10 Fragment：N-terminal peptide MYR MYRISTIC ACID × 1 SOLUTION NMR NMR measurement conditions：pH 5；298 K；Ionic strength (raw mmCIF value) 7；Pressure ambient NMR sample composition：5mM Myristoylated N-terminal Arf6; 5mM acetate buffer, 100mM fully deuterated dodecylphosphocholine (DPC) | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2BAU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E0S small G protein Arf6-GDP Deposited 2000-04-06 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–175（174 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 BME BETA-MERCAPTOETHANOL × 1 NH4 AMMONIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；2M AMMONIUM SULFATE, 0.1M TRIS/HCL PH 8.5
Resolution 2.28 Å R-free 0.234
2A5D Structural basis for the activation of cholera toxin by human ARF6-GTP Deposited 2005-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å R-free 0.199
2A5F Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator, ARF6 Deposited 2005-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.02 Å R-free 0.231
2A5G Cholera toxin A1 subunit bound to ARF6(Q67L) Deposited 2005-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–174（174 aa）
Mutation：Q67L MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.66 Å R-free 0.265
2BAO Solution NMR structure of the myristoylated N-terminal fragment of Arf6 Deposited 2005-10-14 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–10（10 aa） Fragment：N-terminal peptide
Not recorded MYR MYRISTIC ACID × 1 SOLUTION NMR
NMR sample composition 1mM Myristoylated N-terminal Arf6; 5mM acetate buffer | 90% H2O/10% D2O
Resolution not provided
2J5X STRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS Deposited 2006-09-20 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–174（174 aa）
Not recorded GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.60
Resolution 2.80 Å R-free 0.276
2J5X STRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS Deposited 2006-09-20 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–174（174 aa）
Not recorded GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.60
Resolution 2.80 Å R-free 0.276
2W83 Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4 Deposited 2009-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 13–175（163 aa） Fragment：G DOMAIN, RESIDUES 13-175
Chain B 13–175（163 aa） Fragment：G DOMAIN, RESIDUES 13-175
Chain E 13–175（163 aa） Fragment：G DOMAIN, RESIDUES 13-175
Mutation：YES Mutation：YES Mutation：YES GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 DIO 1,4-DIETHYLENE DIOXIDE × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 2.0 M AMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.2 M NACL, 2 MM MGCL2, 6 % MPD
Resolution 1.93 Å R-free 0.238
3LVQ The crystal structure of ASAP3 in complex with Arf6 in transition state Deposited 2010-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain E 11–175（165 aa） Fragment：GAP and Ankyrin domain, residues 416-697, residues 11-175
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.38 Å R-free 0.257
3LVR The crystal structure of ASAP3 in complex with Arf6 in transition state soaked with Calcium Deposited 2010-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain E 11–175（165 aa） Fragment：GAP and Ankyrin domain, residues 416-697, residues 11-175
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5); Crystals were then soaked in 30mM CaCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.38 Å R-free 0.281
3N5C Crystal Structure of Arf6DELTA13 complexed with GDP Deposited 2010-05-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 14–175（162 aa） Fragment：UNP RESIDUES 14-175
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2 M NaCl and 20% PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.82 Å R-free 0.195
3N5C Crystal Structure of Arf6DELTA13 complexed with GDP Deposited 2010-05-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 14–175（162 aa） Fragment：UNP RESIDUES 14-175
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2 M NaCl and 20% PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.82 Å R-free 0.195
3PCR Structure of EspG-Arf6 complex Deposited 2010-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–175（162 aa） Fragment：UNP RESIDUES 14-175
Non-standard monomer：Yes (specific site not provided by mmCIF) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；2% PEG 4000, 0.1 M sodium acetate, 5% 2,3-methylpentanediol, pH 5.0, vapor diffusion, hanging drop, temperature 293K
Resolution 2.50 Å R-free 0.326
4FME EspG-Rab1-Arf6 complex Deposited 2012-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 14–173（160 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；298 K；8% PEG8000, 0.1 M NaKPO4 (pH 6.2), and 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 4.10 Å R-free 0.249
4FME EspG-Rab1-Arf6 complex Deposited 2012-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 14–173（160 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；298 K；8% PEG8000, 0.1 M NaKPO4 (pH 6.2), and 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 4.10 Å R-free 0.249
4KAX Crystal structure of the Grp1 PH domain in complex with Arf6-GTP Deposited 2013-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 14–173（160 aa） Fragment：Arf6 (residues 14-181)
Mutation：Q67L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 CIT CITRIC ACID × 1 GOL GLYCEROL × 4 K POTASSIUM ION × 1 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；50 mM Tris, 20% PEG 4000, 0.2 M sodium citrate. Microseeding and TCEP were needed for large crystal growth, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.235
6BBP Model for compact volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein Deposited 2017-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–173（172 aa）
Mutation：E161A,E161A GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4
Resolution 35.00 Å
6BBQ Model for extended volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A Arf6 Q67L fusion protein Deposited 2017-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–173（172 aa）
Mutation：E161A,E161A GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4
Resolution 35.00 Å
7RK3 Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A Deposited 2021-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–9（8 aa）
Not recorded 4PS 4'-diphospho pantetheine × 1 MYR MYRISTIC ACID × 1 6NA HEXANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20% (w/v) PEG 3350, 200mM ammonium formate
Resolution 2.05 Å R-free 0.220
7XRD Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane Deposited 2022-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–175（174 aa）
Chain B 2–175（174 aa）
Chain C 2–175（174 aa）
Chain D 2–175（174 aa）
Not recorded MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

17 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARF6_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–10； UniProt 1–10

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2bau

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bau
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bau
Deposition date deposition_date2005-10-14
Structure title titleSolution NMR structure of the micelle-bound myristoylated N-terminal Arf6
Keywords keywordsMicelle-bound, myristoylated peptide, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier3.37 Å
Radius of gyration Rg (electron density) rg_electron6.07 Å
Forward intensity I(0) i01708780.00
Molecular weight molecular_weight15104.0 kDa
Excluded volume excluded_volume21075 ų
Envelope volume envelope_volume3401 ų
Hydration-shell volume shell_volume4090 ų
Envelope diameter envelope_diameter29.1 Å
Shell Rg shell_rg12.55 Å
Envelope Rg envelope_rg8.77 Å
Shape Rg shape_rg5.98 Å
Total Rg total_rg7.42 Å
Total atoms total_atoms2388
Residues n_residues120
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax11.7 Å
Rg (real space) rg_real3.71 Å
Rg uncertainty (real space) rg_real_error0.02 Å
I(0) (real space) i0_real1.7640e+06
I(0) uncertainty (real space) i0_real_error9.0930e+03
Rg (reciprocal space) rg_reciprocal2.81 Å
I(0) (reciprocal space) i0_reciprocal1709000.0000
Solution quality estimate total_estimate0.6997
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary4.0 Å
Skewness Skewness skewness0.266
Kurtosis Kurtosis kurtosis-0.645
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha1.5610
Highest regularization parameter α highest_alpha62.8900
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.982; Stabil: 0.912; Sysdev: 0.000; Positv: 1.000; Valcen: 0.769; Smooth: 0.645
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)