SAXSdb — 4fmc

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ROrf2

Escherichia coli

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 47–397	Not recorded	Ras-related protein Rab-1A × 1 （P62820） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 47–397	Not recorded	Ras-related protein Rab-1A × 1 （P62820） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 47–397	Not recorded	Ras-related protein Rab-1A × 1 （P62820） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	O52121_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–351； UniProt 47–397 Author chain C； PDBConstruct 1–351； UniProt 47–397 Author chain E； 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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 6–176	Not recorded	ROrf2 × 1 （O52121） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 6–176	Not recorded	ROrf2 × 1 （O52121） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 14–115	Not recorded	ROrf2 × 1 （O52121） 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

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 4FMC	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 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 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 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 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 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 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 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 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
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16	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 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 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
4FME EspG-Rab1-Arf6 complex Deposited 2012-06-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 6–176（171 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 6–176（171 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
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 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 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 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 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 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAB1A_HUMAN
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–171； UniProt 6–176 Author chain D； PDBConstruct 1–171； UniProt 6–176 Author chain F； PDBConstruct 1–102； UniProt 14–115

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4fmc
Deposition date deposition_date	2012-06-16
Structure title title	EspG-Rab1 complex
Keywords keywords	alpha-beta fold, Rab1-GAP, Rab1, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.59 Å
Radius of gyration Rg (electron density) rg_electron	37.90 Å
Forward intensity I(0) i0	431563000.00
Molecular weight molecular_weight	163610.0 kDa
Excluded volume excluded_volume	202540 Å³
Envelope volume envelope_volume	267090 Å³
Hydration-shell volume shell_volume	57967 Å³
Envelope diameter envelope_diameter	136.7 Å
Shell Rg shell_rg	44.50 Å
Envelope Rg envelope_rg	37.68 Å
Shape Rg shape_rg	37.89 Å
Total Rg total_rg	38.30 Å
Total atoms total_atoms	11465
Residues n_residues	1464
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	128.2 Å
Rg (real space) rg_real	38.52 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	4.3160e+08
I(0) uncertainty (real space) i0_real_error	7.2000e+06
Rg (reciprocal space) rg_reciprocal	38.57 Å
I(0) (reciprocal space) i0_reciprocal	431600000.0000
Solution quality estimate total_estimate	0.8878
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.9 Å
Skewness Skewness skewness	0.271
Kurtosis Kurtosis kurtosis	-0.420
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	134800000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.880

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	ROrf2
Molecular weight formula_weight	38915.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	11470

EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCIIDEMVRALQPRYAASETYLQN

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-1A
Molecular weight formula_weight	19477.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ras-related protein Rab-1A
Molecular weight formula_weight	13289.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

LLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4fmcb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4fmcd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (5 domains)

Domain ID domain_id	4fmcA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	460 — EspG protein, N-terminal domain

Domain ID domain_id	4fmcB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4fmcC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	460 — EspG protein, N-terminal domain

Domain ID domain_id	4fmcD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4fmcE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	460 — EspG protein, N-terminal domain

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8. Citations (1)

▶

Unit-cell length a length_a	107.566 Å
Unit-cell length b length_b	152.707 Å
Unit-cell length c length_c	226.706 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2770

fit	/app/data/saxs_computation/fm/4fmc/4fmc.fit
pddf	/app/data/pr_computation/fm/4fmc/4fmc.pr.out
profile	/app/data/saxs_computation/fm/4fmc/4fmc.dat

EspG-Rab1 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

ROrf2

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-1A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)