1r4a

Crystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP Domain of Golgin245 COMPLEX

Method: X-RAY DIFFRACTION D_max: 118.5 Å Quality: GOOD

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

ADP-ribosylation factor-like protein 1

Rattus norvegicus

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 16–180 Chain B； UniProt 16–180 Chain C； UniProt 16–180 Chain D； UniProt 16–180	Fragment：Arl1 (Residue 16-180)	Golgi autoantigen, golgin subfamily A member 4 × 4 （Q13439） MG MAGNESIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG3350, potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.30 Å R-free 0.260

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	ARL1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 16–180 Author chain B； PDBConstruct 1–165； UniProt 16–180 Author chain C； PDBConstruct 1–165； UniProt 16–180 Author chain D； PDBConstruct 1–165； UniProt 16–180

Golgi autoantigen, golgin subfamily A member 4

Homo sapiens

UniProt Q13439

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain E； UniProt 2172–2222 Chain F； UniProt 2172–2222 Chain G； UniProt 2172–2222 Chain H； UniProt 2172–2222	Fragment：GRIP Domain (Residue 2172-2222)	ADP-ribosylation factor-like protein 1 × 4 （P61212） MG MAGNESIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG3350, potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.30 Å R-free 0.260

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1R4A	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 B 2170–2228（59 aa） Fragment：GRIP DOMAIN RESIDUES 2170-2228 Chain D 2170–2228（59 aa） Fragment：GRIP DOMAIN RESIDUES 2170-2228	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 F 2170–2228（59 aa） Fragment：GRIP DOMAIN RESIDUES 2170-2228 Chain H 2170–2228（59 aa） Fragment：GRIP DOMAIN RESIDUES 2170-2228	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

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

View Construct and Data Evidence

UniProt name	GOGA4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–51； UniProt 2172–2222 Author chain F； PDBConstruct 1–51； UniProt 2172–2222 Author chain G； PDBConstruct 1–51； UniProt 2172–2222 Author chain H； PDBConstruct 1–51； UniProt 2172–2222

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1r4a
Deposition date deposition_date	2003-10-04
Structure title title	Crystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP Domain of Golgin245 COMPLEX
Keywords keywords	Ras-like G Protein structure, Three-helix GRIP domain, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	36.74 Å
Radius of gyration Rg (electron density) rg_electron	35.96 Å
Forward intensity I(0) i0	159977000.00
Molecular weight molecular_weight	101740.0 kDa
Excluded volume excluded_volume	127650 Å³
Envelope volume envelope_volume	174320 Å³
Hydration-shell volume shell_volume	41728 Å³
Envelope diameter envelope_diameter	122.1 Å
Shell Rg shell_rg	40.98 Å
Envelope Rg envelope_rg	34.90 Å
Shape Rg shape_rg	35.94 Å
Total Rg total_rg	36.41 Å
Total atoms total_atoms	7112
Residues n_residues	864
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	118.5 Å
Rg (real space) rg_real	36.67 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	1.6000e+08
I(0) uncertainty (real space) i0_real_error	2.4710e+06
Rg (reciprocal space) rg_reciprocal	36.72 Å
I(0) (reciprocal space) i0_reciprocal	160000000.0000
Solution quality estimate total_estimate	0.8936
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.4 Å
Skewness Skewness skewness	0.166
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23590000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.881

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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	18737.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7380

REMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Golgi autoantigen, golgin subfamily A member 4
Molecular weight formula_weight	6198.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

PTEFEYLRKVLFEYMMGRETKTMAKVITTVLKFPDDQTQKILEREDARLMF

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	4

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	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1r4aa_
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	d1r4ab_
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	d1r4ac_
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	d1r4ad_
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	d1r4ae_
Class class	a — All alpha proteins
Fold Fold fold	a.193 — GRIP domain
Superfamily Superfamily superfamily	a.193.1 — GRIP domain
Family Family family	a.193.1.1 — GRIP domain

Domain ID domain_id	d1r4af_
Class class	a — All alpha proteins
Fold Fold fold	a.193 — GRIP domain
Superfamily Superfamily superfamily	a.193.1 — GRIP domain
Family Family family	a.193.1.1 — GRIP domain

Domain ID domain_id	d1r4ag_
Class class	a — All alpha proteins
Fold Fold fold	a.193 — GRIP domain
Superfamily Superfamily superfamily	a.193.1 — GRIP domain
Family Family family	a.193.1.1 — GRIP domain

Domain ID domain_id	d1r4ah_
Class class	a — All alpha proteins
Fold Fold fold	a.193 — GRIP domain
Superfamily Superfamily superfamily	a.193.1 — GRIP domain
Family Family family	a.193.1.1 — GRIP domain

CATH v4.4 (8 domains)

Domain ID domain_id	1r4aA00
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	1r4aB00
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	1r4aC00
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	1r4aD00
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	1r4aE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	60 — GRIP domain

Domain ID domain_id	1r4aF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	60 — GRIP domain

Domain ID domain_id	1r4aG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	60 — GRIP domain

Domain ID domain_id	1r4aH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	60 — GRIP domain

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8. Citations (1)

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Unit-cell length a length_a	42.083 Å
Unit-cell length b length_b	86.924 Å
Unit-cell length c length_c	86.246 Å
Unit-cell angle α angle_alpha	118.11 °
Unit-cell angle β angle_beta	99.65 °
Unit-cell angle γ angle_gamma	95.47 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2508
R_work r_work	0.2463
R_free r_free	0.2601

fit	/app/data/saxs_computation/r4/1r4a/1r4a.fit
pddf	/app/data/pr_computation/r4/1r4a/1r4a.pr.out
profile	/app/data/saxs_computation/r4/1r4a/1r4a.dat

Crystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP Domain of Golgin245 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

Golgi autoantigen, golgin subfamily A member 4

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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)