SAXSdb — 5j5c

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

ADP-ribosylation factor-like protein 1

Homo sapiens

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 16–181	Fragment：small GTPase, UNP residues 16-181 Mutation：Q71L	Brefeldin A-inhibited guanine nucleotide-exchange protein 1 × 1 （Q9Y6D6） MG MAGNESIUM ION × 1 SO4 SULFATE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.1；289 K；0.2M lithium sulfate, 0.1M sodium citrate tribasic, 0.1M Tris-HCl pH 9.1, and 27% (w/v) polyethylene glycol 3350	Resolution 3.40 Å R-free 0.258

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 5J5C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UPT Structure of a complex of the golgin-245 GRIP domain with Arl1 Deposited 2003-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 15–181（167 aa） Fragment：RESIDUES 15-181 Chain C 15–181（167 aa） Fragment：RESIDUES 15-181	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；GROWTH IN 20% PEG 3350, 0.2M TRIS-HCL PH 8.5. RESERVOIR EXCHANGED FOR 31% PEG 3350, 31% PEG 3350, 0.2M TRIS-HCL PH 8.5, FROZEN IN 31% PEG 3350, 0.2M TRIS-HCL PH 8.5.	Resolution 1.70 Å R-free 0.252
1UPT Structure of a complex of the golgin-245 GRIP domain with Arl1 Deposited 2003-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 15–181（167 aa） Fragment：RESIDUES 15-181 Chain G 15–181（167 aa） Fragment：RESIDUES 15-181	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；GROWTH IN 20% PEG 3350, 0.2M TRIS-HCL PH 8.5. RESERVOIR EXCHANGED FOR 31% PEG 3350, 31% PEG 3350, 0.2M TRIS-HCL PH 8.5, FROZEN IN 31% PEG 3350, 0.2M TRIS-HCL PH 8.5.	Resolution 1.70 Å R-free 0.252
4DCN Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1 Deposited 2012-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 14–179（166 aa） Fragment：N-terminus truncated Arl1, residues 14-179 Chain B 14–179（166 aa） Fragment：N-terminus truncated Arl1, residues 14-179	Mutation：Q71L Mutation：Q71L	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；100mM HEPES, 200mM Ammonium Sulfate, 25%(w/v) PEG3350, pH 7.5, vapor diffusion, temperature 298K	Resolution 3.01 Å R-free 0.333
5EE5 Structure of human ARL1 in complex with the DCB domain of BIG1 Deposited 2015-10-22	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 15–181（167 aa）	Mutation：delta N14, Q71L	NA SODIUM ION × 14 GOL GLYCEROL × 2 CL CHLORIDE ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 8K/PEG 1k 10% Sodium Acetate 0.1-0.2mM Tris pH8.5 glacial acetic 0.100mM	Resolution 2.28 Å R-free 0.259

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–168； UniProt 16–181

Brefeldin A-inhibited guanine nucleotide-exchange protein 1

Homo sapiens

UniProt Q9Y6D6

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 1–224	Fragment：DCB domain, UNP residues 1-224	ADP-ribosylation factor-like protein 1 × 1 （P40616） MG MAGNESIUM ION × 1 SO4 SULFATE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.1；289 K；0.2M lithium sulfate, 0.1M sodium citrate tribasic, 0.1M Tris-HCl pH 9.1, and 27% (w/v) polyethylene glycol 3350	Resolution 3.40 Å R-free 0.258

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 5J5C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LTL Crystal structure of human BIG1 Sec7 domain Deposited 2010-02-16	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 691–889（199 aa） Fragment：Sec7 domain	Not recorded	CA CALCIUM ION × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；30% PEG 3350, 0.2M sodium acetate, 0.2M tris pH 7.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.20 Å R-free 0.236
3LTL Crystal structure of human BIG1 Sec7 domain Deposited 2010-02-16	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 691–889（199 aa） Fragment：Sec7 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；30% PEG 3350, 0.2M sodium acetate, 0.2M tris pH 7.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.20 Å R-free 0.236
5EE5 Structure of human ARL1 in complex with the DCB domain of BIG1 Deposited 2015-10-22	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 1–229（229 aa）	Mutation：delta-52-70 Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 14 GOL GLYCEROL × 2 CL CHLORIDE ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 8K/PEG 1k 10% Sodium Acetate 0.1-0.2mM Tris pH8.5 glacial acetic 0.100mM	Resolution 2.28 Å R-free 0.259

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BIG1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–224； UniProt 1–224

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	5j5c
Deposition date deposition_date	2016-04-02
Structure title title	Crystal structure of ARL1-GTP and DCB domain of BIG1 complex
Keywords keywords	small GTPase, effector, GEF, SIGNALING PROTEIN; SIGNALING PROTEIN
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	22.38 Å
Radius of gyration Rg (electron density) rg_electron	21.25 Å
Forward intensity I(0) i0	27027800.00
Molecular weight molecular_weight	38845.0 kDa
Excluded volume excluded_volume	48306 Å³
Envelope volume envelope_volume	59742 Å³
Hydration-shell volume shell_volume	23416 Å³
Envelope diameter envelope_diameter	72.8 Å
Shell Rg shell_rg	27.92 Å
Envelope Rg envelope_rg	21.65 Å
Shape Rg shape_rg	21.26 Å
Total Rg total_rg	22.09 Å
Total atoms total_atoms	2717
Residues n_residues	359
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	70.5 Å
Rg (real space) rg_real	22.32 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	2.7030e+07
I(0) uncertainty (real space) i0_real_error	3.5360e+05
Rg (reciprocal space) rg_reciprocal	22.34 Å
I(0) (reciprocal space) i0_reciprocal	27030000.0000
Solution quality estimate total_estimate	0.9029
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.258
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5308000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ADP-ribosylation factor-like protein 1
Molecular weight formula_weight	19045.0 kDa
Mutation mutation	Q71L
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2717

MGREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSRQ

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 2 Entity 2 polymer

Description description	Brefeldin A-inhibited guanine nucleotide-exchange protein 1
Molecular weight formula_weight	24981.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MYEGKKTKNMFLTRALEKILADKEVKKAHHSQLRKACEVALEEIKAETEKQSPPHGEAKAGSSTLPPVKSKTNFIEADKYFLPFELACQSKCPRIVSTSLDCLQKLIAYGHLTGNAPDSTTPGKKLIDRIIETICGCFQGPQTDEGVQLQIIKALLTAVTSQHIEIHEGTVLQAVRTCYNIYLASKNLINQTTAKATLTQMLNVIFARMENQALQEAKQMEKER

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 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5j5cA00
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

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8. Citations (1)

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Unit-cell length a length_a	107.819 Å
Unit-cell length b length_b	107.819 Å
Unit-cell length c length_c	204.627 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2267
R_work r_work	0.2249
R_free r_free	0.2581

fit	/app/data/saxs_computation/j5/5j5c/5j5c.fit
pddf	/app/data/pr_computation/j5/5j5c/5j5c.pr.out
profile	/app/data/saxs_computation/j5/5j5c/5j5c.dat

Crystal structure of ARL1-GTP and DCB domain of BIG1 complex

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

ADP-ribosylation factor-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Brefeldin A-inhibited guanine nucleotide-exchange protein 1

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)