SAXSdb — 4dcn

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 14–179 Chain B； UniProt 14–179	Fragment：N-terminus truncated Arl1, residues 14-179 Mutation：Q71L	Arfaptin-2 × 2 （P53365） 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

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 4DCN	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 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 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
5EE5 Structure of human ARL1 in complex with the DCB domain of BIG1 Deposited 2015-10-22	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 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
5J5C Crystal structure of ARL1-GTP and DCB domain of BIG1 complex Deposited 2016-04-02	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 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 14–179 Author chain B； PDBConstruct 1–166； UniProt 14–179

Arfaptin-2

Homo sapiens

UniProt P53365

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 118–315 Chain D； UniProt 118–315	Fragment：C-terminal BAR domain, residues 118-315	ADP-ribosylation factor-like protein 1 × 2 （P40616） 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

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 4DCN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I49 CRYSTAL STRUCTURE ANALYSIS OF ARFAPTIN Deposited 2001-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；TRI-SODIUM CITRATE DIHYDRATE, ISOPROPANOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.275
1I4D CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21) Deposited 2001-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, Peg20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.298
1I4L CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41) Deposited 2001-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.301
1I4L CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41) Deposited 2001-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.301
1I4T CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN Deposited 2001-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.304
1I4T CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN Deposited 2001-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.304
2DCO S1P4 First Extracellular Loop Peptidomimetic Deposited 2006-01-11	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 235–244（10 aa） Fragment：Extracellular Loop 1 Chain A 260–261（2 aa） Fragment：Extracellular Loop 1 Chain A 264–267（4 aa） Fragment：Extracellular Loop 1	Mutation：L10C/A28C Mutation：L10C/A28C Mutation：L10C/A28C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 0.06 mol/kg；Pressure 1 NMR sample composition 1mM CCE1a U-15N; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN3 \| 20% TFE-d3 NMR sample composition 3mM CCE1a U-15N,13C; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN3 \| 20% TFE-d3	Resolution not provided

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

View Construct and Data Evidence

UniProt name	ARFP2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–198； UniProt 118–315 Author chain D； PDBConstruct 1–198； UniProt 118–315

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	4dcn
Deposition date deposition_date	2012-01-18
Structure title title	Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1
Keywords keywords	Small GTPase Effector Complex, BAR domain, Membrane deformation, PROTEIN BINDING-SIGNALING PROTEIN complex; PROTEIN BINDING/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	42.27 Å
Radius of gyration Rg (electron density) rg_electron	42.21 Å
Forward intensity I(0) i0	104020000.00
Molecular weight molecular_weight	82657.0 kDa
Excluded volume excluded_volume	103600 Å³
Envelope volume envelope_volume	145340 Å³
Hydration-shell volume shell_volume	32033 Å³
Envelope diameter envelope_diameter	153.3 Å
Shell Rg shell_rg	41.25 Å
Envelope Rg envelope_rg	42.43 Å
Shape Rg shape_rg	42.19 Å
Total Rg total_rg	42.22 Å
Total atoms total_atoms	5801
Residues n_residues	719
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	146.7 Å
Rg (real space) rg_real	42.73 Å
Rg uncertainty (real space) rg_real_error	2.21 Å
I(0) (real space) i0_real	1.0400e+08
I(0) uncertainty (real space) i0_real_error	2.0480e+06
Rg (reciprocal space) rg_reciprocal	42.27 Å
I(0) (reciprocal space) i0_reciprocal	104000000.0000
Solution quality estimate total_estimate	0.7531
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.441
Kurtosis Kurtosis kurtosis	-0.734
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4789000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.525; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.422; Smooth: 0.789

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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	18729.6 kDa
Mutation mutation	Q71L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5805

GTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKS

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	Arfaptin-2
Molecular weight formula_weight	22548.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSRTVDLELELQIELLRETKRKYESVLQLGRALTAHLYSLLQTQHALGDAFADLSQKSPELQEEFGYNAETQKLLCKNGETLLGAVNFFVSSINTLVTKTMEDTLMTVKQYEAARLEYDAYRTDLEELSLGPRDAGTRGRLESAQATFQAHRDKYEKLRGDVAIKLKFLEENKIKVMHKQLLLFHNAVSAYFAGNQKQ

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	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4dcna_
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	d4dcnb_
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	d4dcnc_
Class class	a — All alpha proteins
Fold Fold fold	a.238 — BAR/IMD domain-like
Superfamily Superfamily superfamily	a.238.1 — BAR/IMD domain-like
Family Family family	a.238.1.2 — Arfaptin, Rac-binding fragment

Domain ID domain_id	d4dcnd_
Class class	a — All alpha proteins
Fold Fold fold	a.238 — BAR/IMD domain-like
Superfamily Superfamily superfamily	a.238.1 — BAR/IMD domain-like
Family Family family	a.238.1.2 — Arfaptin, Rac-binding fragment

CATH v4.4 (4 domains)

Domain ID domain_id	4dcnA00
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	4dcnB00
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	4dcnC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4dcnD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

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8. Citations (1)

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Unit-cell length a length_a	62.764 Å
Unit-cell length b length_b	111.125 Å
Unit-cell length c length_c	119.809 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2642
R_free r_free	0.3330

fit	/app/data/saxs_computation/dc/4dcn/4dcn.fit
pddf	/app/data/pr_computation/dc/4dcn/4dcn.pr.out
profile	/app/data/saxs_computation/dc/4dcn/4dcn.dat

Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1

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

Arfaptin-2

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 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)