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4fme

EspG-Rab1-Arf6 complex

Method: X-RAY DIFFRACTION Dmax: 110.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EspG protein

Escherichia coli

UniProt Q5WMC0

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 47–397 Not recorded Ras-related protein Rab-1A × 1 （P62820） ADP-ribosylation factor 6 × 1 （P62330） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 47–397 Not recorded Ras-related protein Rab-1A × 1 （P62820） ADP-ribosylation factor 6 × 1 （P62330） 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

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 4FME Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 2 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain K 47–397（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 13 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 47–397（351 aa）
Chain C 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 4 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 14 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 47–397（351 aa）
Chain F 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 15 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 47–397（351 aa）
Chain K 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 16 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 47–397（351 aa）
Chain I 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 17 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 47–397（351 aa）
Chain L 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 18 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain H 47–397（351 aa）
Chain J 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 47–397（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMA EspG structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 47–397（351 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.239
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 47–397（351 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.05 Å R-free 0.266
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 47–397（351 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.05 Å R-free 0.266
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 47–397（351 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.05 Å R-free 0.266

2 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5WMC0_ECOLX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–351； UniProt 47–397 Author chain D； PDBConstruct 1–351； UniProt 47–397

Ras-related protein Rab-1A

Homo sapiens

UniProt P62820

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 6–176 Not recorded EspG protein × 1 （Q5WMC0） ADP-ribosylation factor 6 × 1 （P62330） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 6–176 Not recorded EspG protein × 1 （Q5WMC0） ADP-ribosylation factor 6 × 1 （P62330） 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

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 4FME Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2FOL Crystal structure of human RAB1A in complex with GDP Deposited 2006-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 5–176（172 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Resolution 2.63 Å R-free 0.252
2WWX Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex Deposited 2009-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 4–178（175 aa） Fragment：GTPASE DOMAIN, RESIDUES 4-178
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.231
3L0I Complex structure of SidM/DrrA with the wild type Rab1 Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–177（177 aa） Fragment：small GTPase domain, residues 1-177
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.266
3L0I Complex structure of SidM/DrrA with the wild type Rab1 Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–177（177 aa） Fragment：small GTPase domain, residues 1-177
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.266
3SFV Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila Deposited 2011-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–176（176 aa） Fragment：residues 1-176
Mutation：S25N GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；293 K；28% Jeffamin ED-2001, 0.1M sodium citrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.73 Å R-free 0.228
3TKL Crystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA from Legionella pneumophila Deposited 2011-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–191（191 aa） Fragment：UNP residues 1-191
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 25% PEG3350, 0.7% butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.18 Å R-free 0.252
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 6–176（171 aa）
Chain D 6–176（171 aa）
Chain F 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMC EspG-Rab1 complex Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–176（171 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.277
4FMC EspG-Rab1 complex Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.277
4FMC EspG-Rab1 complex Deposited 2012-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 14–115（102 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.277
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.05 Å R-free 0.266
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 6–176（171 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.05 Å R-free 0.266
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 13–176（164 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.05 Å R-free 0.266
4IRU Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 Deposited 2013-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–177（174 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ACT ACETATE ION × 4 GOL GLYCEROL × 7 K POTASSIUM ION × 5 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.288
4IRU Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 Deposited 2013-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 4–177（174 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ACT ACETATE ION × 8 GOL GLYCEROL × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.288
4IRU Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 Deposited 2013-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 4–177（174 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.288
4JVS Crystal structure of LepB GAP domain from Legionella drancourtii in complex with Rab1-GDP and AlF3 Deposited 2013-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–177（177 aa） Fragment：UNP residues 1-177
Not recorded ACY ACETIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；298 K；0.2M ammonium acetate, 0.1M Tris, 25%(w/v) polyethylene glycol 3350, pH 8.5, EVAPORATION, temperature 298.0K
Resolution 2.78 Å R-free 0.265
7EQ2 Crystal structure of GDP-bound Rab1a-T75D Deposited 2021-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–176（176 aa）
Mutation：T75D GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NCO COBALT HEXAMMINE(III) × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291.15 K；40mM Lithium chloride, 20mM Magnesium chloride hexahydrate, 80mM NaCl, 2mM Hexammine cobalt(III) chloride, 40mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 1.55 Å R-free 0.185
7EQ2 Crystal structure of GDP-bound Rab1a-T75D Deposited 2021-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–176（176 aa）
Mutation：T75D GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NCO COBALT HEXAMMINE(III) × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CAC CACODYLATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291.15 K；40mM Lithium chloride, 20mM Magnesium chloride hexahydrate, 80mM NaCl, 2mM Hexammine cobalt(III) chloride, 40mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 1.55 Å R-free 0.185
9MHF Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L) Deposited 2024-12-11 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 E 1–205（205 aa）
Mutation：Q70L GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
9MHG Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation Deposited 2024-12-11 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 E 1–205（205 aa）
Mutation：Q70L GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05%
cryo-EM vitrification conditions Cryogen ETHANE；100% humidity, 3 s wait time, blot force -15
Resolution 3.20 Å
9MHH PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation Deposited 2024-12-11 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 E 1–205（205 aa）
Mutation：Q70L GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05%
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å

14 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAB1A_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–171； UniProt 6–176 Author chain E； PDBConstruct 1–171； UniProt 6–176

ADP-ribosylation factor 6

Homo sapiens

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 14–173 Not recorded EspG protein × 1 （Q5WMC0） Ras-related protein Rab-1A × 1 （P62820） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain F； UniProt 14–173 Not recorded EspG protein × 1 （Q5WMC0） Ras-related protein Rab-1A × 1 （P62820） 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

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 4FME 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 oligomeric state Different ligand/ion 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 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 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 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 construct Different oligomeric state 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 1–10（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
2BAU Solution NMR structure of the micelle-bound myristoylated N-terminal Arf6 Deposited 2005-10-14 Different construct Different oligomeric state 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 1–10（10 aa） Fragment：N-terminal peptide
Not recorded 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
2J5X STRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS Deposited 2006-09-20 Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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
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 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 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 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARF6_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–160； UniProt 14–173 Author chain F； PDBConstruct 1–160； UniProt 14–173

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 4fme

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fme
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fme
Deposition date deposition_date2012-06-16
Structure title titleEspG-Rab1-Arf6 complex
Keywords keywordsalpha-beta fold, Rab1-GAP, Arf6 effector, Rab1, Arf6, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.33 Å
Radius of gyration Rg (electron density) rg_electron34.54 Å
Forward intensity I(0) i0391881000.00
Molecular weight molecular_weight155580.0 kDa
Excluded volume excluded_volume193040 ų
Envelope volume envelope_volume249980 ų
Hydration-shell volume shell_volume57900 ų
Envelope diameter envelope_diameter118.2 Å
Shell Rg shell_rg42.86 Å
Envelope Rg envelope_rg34.11 Å
Shape Rg shape_rg34.54 Å
Total Rg total_rg35.12 Å
Total atoms total_atoms10906
Residues n_residues1364
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 dmax110.4 Å
Rg (real space) rg_real35.10 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real3.9190e+08
I(0) uncertainty (real space) i0_real_error6.8620e+06
Rg (reciprocal space) rg_reciprocal35.25 Å
I(0) (reciprocal space) i0_reciprocal391900000.0000
Solution quality estimate total_estimate0.8975
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.1 Å
Skewness Skewness skewness0.073
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha123500000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.975
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)