SAXSdb — 5ee5

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

Brefeldin A-inhibited guanine nucleotide-exchange 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 1–229	Mutation：delta-52-70 Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP-ribosylation factor-like protein 1 × 1 （P40616） 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

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 5EE5	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 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 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 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 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
5J5C Crystal structure of ARL1-GTP and DCB domain of BIG1 complex Deposited 2016-04-02	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 1–224（224 aa） Fragment：DCB domain, UNP residues 1-224	Not recorded	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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–213； UniProt 1–229

ADP-ribosylation factor-like protein 1

Homo sapiens

UniProt P40616

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 15–181	Mutation：delta N14, Q71L	Brefeldin A-inhibited guanine nucleotide-exchange protein 1 × 1 （Q9Y6D6） 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

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 5EE5	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
5J5C Crystal structure of ARL1-GTP and DCB domain of BIG1 complex Deposited 2016-04-02	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 16–181（166 aa） Fragment：small GTPase, UNP residues 16-181	Mutation：Q71L	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

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	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–171； UniProt 15–181

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	5ee5
Deposition date deposition_date	2015-10-22
Structure title title	Structure of human ARL1 in complex with the DCB domain of BIG1
Keywords keywords	ARF1-GEF ARL1-effector Trans-golgi DCB domain, transcription; TRANSCRIPTION
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	23.12 Å
Radius of gyration Rg (electron density) rg_electron	22.08 Å
Forward intensity I(0) i0	30352400.00
Molecular weight molecular_weight	42768.0 kDa
Excluded volume excluded_volume	53732 Å³
Envelope volume envelope_volume	66317 Å³
Hydration-shell volume shell_volume	24960 Å³
Envelope diameter envelope_diameter	82.8 Å
Shell Rg shell_rg	28.84 Å
Envelope Rg envelope_rg	22.65 Å
Shape Rg shape_rg	22.07 Å
Total Rg total_rg	22.98 Å
Total atoms total_atoms	2968
Residues n_residues	365
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	77.5 Å
Rg (real space) rg_real	23.07 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	3.0350e+07
I(0) uncertainty (real space) i0_real_error	4.4450e+05
Rg (reciprocal space) rg_reciprocal	23.08 Å
I(0) (reciprocal space) i0_reciprocal	30350000.0000
Solution quality estimate total_estimate	0.8035
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.6 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5376000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Brefeldin A-inhibited guanine nucleotide-exchange protein 1
Molecular weight formula_weight	24173.0 kDa
Mutation mutation	delta-52-70
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	3009

GSHMYEGKKTKNMFLTRALEKILADKEVKKAHHSQLRKACEVALEEIKAETEKQKTNFIEADKYFLPFELACQSKCPRIVSTSLDCLQKLIAYGHLTGNAPDSTTPGKKLIDRIIETICGCFQGPQTDEGVQLQIIKALLTAVTSQHIEIHEGTVLQAVRTCYNIYLASKNLINQTTAKATLTQMLNVIFARMENQALQEAKQMEKERHRQHH

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	ADP-ribosylation factor-like protein 1
Molecular weight formula_weight	19371.3 kDa
Mutation mutation	delta N14, Q71L
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSRQ

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 BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

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

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	4

Entity 8 Entity 8 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5ee5b_
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 (1 domains)

Domain ID domain_id	5ee5B00
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	84.166 Å
Unit-cell length b length_b	50.727 Å
Unit-cell length c length_c	103.837 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.279 Å
Low-resolution limit resolution_low	29.069 Å
R factor r_factor	0.2193
R_work r_work	0.2172
R_free r_free	0.2590

fit	/app/data/saxs_computation/ee/5ee5/5ee5.fit
pddf	/app/data/pr_computation/ee/5ee5/5ee5.pr.out
profile	/app/data/saxs_computation/ee/5ee5/5ee5.dat

Structure of human ARL1 in complex with the DCB domain of BIG1

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

Brefeldin A-inhibited guanine nucleotide-exchange protein 1

State in the Current Structure

Other States of the Same Protein in the Database

ADP-ribosylation factor-like 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 (9)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)