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3dof

Complex of ARL2 and BART, Crystal Form 2

Method: X-RAY DIFFRACTION Dmax: 76.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-ribosylation factor-like protein 2

Homo sapiens

UniProt P36404

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 1–184 Not recorded ADP-ribosylation factor-like protein 2-binding protein × 1 （Q9Y2Y0） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；0.2M MgCl2, 20% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.30 Å R-free 0.294

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 3DOF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DOE Complex of ARL2 and BART, Crystal Form 1 Deposited 2008-07-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–184（184 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；0.1M bicine, 10% PEG 6000, 20mM hexammine cobalt (III) chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.25 Å R-free 0.261
9M1I Cryo-EM structure of the TBC-D-Arl2-beta-tubulin complex Deposited 2025-02-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–184（184 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
9M1J Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex Deposited 2025-02-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–184（184 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.14 Å
9M1K Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex with GTP Deposited 2025-02-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–184（184 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
9M1L Cryo-EM structure of the TBC-DE-Arl2-alpha-beta-tubulin complex with GTP Deposited 2025-02-26 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 G 1–184（184 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
9M1M Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx Deposited 2025-02-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–184（184 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.21 Å
9M1N Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx Deposited 2025-02-26 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 G 1–184（184 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–184； UniProt 1–184

ADP-ribosylation factor-like protein 2-binding protein

Homo sapiens

UniProt Q9Y2Y0

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 1–163 Not recorded ADP-ribosylation factor-like protein 2 × 1 （P36404） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；0.2M MgCl2, 20% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.30 Å R-free 0.294

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 3DOF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2K9A The Solution Structure of the Arl2 Effector, BART Deposited 2008-10-06 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 1–136（136 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3DOE Complex of ARL2 and BART, Crystal Form 1 Deposited 2008-07-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–163（163 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；0.1M bicine, 10% PEG 6000, 20mM hexammine cobalt (III) chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.25 Å R-free 0.261

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

View Construct and Data Evidence
UniProt name AR2BP_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–165； UniProt 1–163

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 3dof

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dof
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dof
Deposition date deposition_date2008-07-04
Structure title titleComplex of ARL2 and BART, Crystal Form 2
Keywords keywords;ADP-ribosylation factor-like 2, binder of ARL2, small GTPase, effector, complex structure, GTP-binding, Lipoprotein, Myristate, Nucleotide-binding, Polymorphism, Alternative splicing, Cytoplasm, Mitochondrion, Phosphoprotein, SIGNALING PROTEIN-HYDROLASE COMPLEX ;; SIGNALING PROTEIN/HYDROLASE
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_guinier23.27 Å
Radius of gyration Rg (electron density) rg_electron22.14 Å
Forward intensity I(0) i023140800.00
Molecular weight molecular_weight36373.0 kDa
Excluded volume excluded_volume45388 ų
Envelope volume envelope_volume55919 ų
Hydration-shell volume shell_volume21712 ų
Envelope diameter envelope_diameter79.0 Å
Shell Rg shell_rg28.19 Å
Envelope Rg envelope_rg22.23 Å
Shape Rg shape_rg22.14 Å
Total Rg total_rg22.93 Å
Total atoms total_atoms2559
Residues n_residues309
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 dmax76.2 Å
Rg (real space) rg_real23.26 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real2.3140e+07
I(0) uncertainty (real space) i0_real_error3.0320e+05
Rg (reciprocal space) rg_reciprocal23.27 Å
I(0) (reciprocal space) i0_reciprocal23140000.0000
Solution quality estimate total_estimate0.8934
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4181000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.962
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3dofA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3dofB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1520 — Adp-ribosylation factor-like protein 2-binding protein fold
Homologous superfamily homologous superfamily10 — ADP-ribosylation factor-like 2-binding protein, domain
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8. Citations (1)

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9. Files and Curves (10)