1upt

Structure of a complex of the golgin-245 GRIP domain with Arl1

Method: X-RAY DIFFRACTION D_max: 134.8 Å Quality: GOOD

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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 15–181 Chain C； UniProt 15–181	Fragment：RESIDUES 15-181 Non-standard monomer：Yes (specific site not provided by mmCIF)	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4 × 2 （Q13439） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 15–181 Chain G； UniProt 15–181	Fragment：RESIDUES 15-181 Non-standard monomer：Yes (specific site not provided by mmCIF)	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4 × 2 （Q13439） 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

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 1UPT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DCN Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1 Deposited 2012-01-18	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 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 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 3 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 5–171； UniProt 15–181 Author chain C； PDBConstruct 5–171； UniProt 15–181 Author chain E； PDBConstruct 5–171； UniProt 15–181 Author chain G； PDBConstruct 5–171； UniProt 15–181

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 2170–2228 Chain D； UniProt 2170–2228	Fragment：GRIP DOMAIN RESIDUES 2170-2228 Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1 × 2 （P40616） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 2170–2228 Chain H； UniProt 2170–2228	Fragment：GRIP DOMAIN RESIDUES 2170-2228 Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1 × 2 （P40616） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1UPT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1R4A Crystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP Domain of Golgin245 COMPLEX Deposited 2003-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2172–2222（51 aa） Fragment：GRIP Domain (Residue 2172-2222) Chain F 2172–2222（51 aa） Fragment：GRIP Domain (Residue 2172-2222) Chain G 2172–2222（51 aa） Fragment：GRIP Domain (Residue 2172-2222) Chain H 2172–2222（51 aa） Fragment：GRIP Domain (Residue 2172-2222)	Not recorded	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

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

View Construct and Data Evidence

UniProt name	GOA4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–60； UniProt 2170–2228 Author chain D； PDBConstruct 2–60； UniProt 2170–2228 Author chain F； PDBConstruct 2–60； UniProt 2170–2228 Author chain H； PDBConstruct 2–60； UniProt 2170–2228

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	1upt
Deposition date deposition_date	2003-10-12
Structure title title	Structure of a complex of the golgin-245 GRIP domain with Arl1
Keywords keywords	;HYDROLASE/PROTEIN-BINDING, COMPLEX (GTPASE-GOLGIN), GOLGIN-245, GRIP, ARL1, GOLGIN, GTPASE, G-PROTEIN, GOLGI, GRIP DIMER, PROTEIN SORTING, VESICLE TRAFFICKING, HYDROLASE-PROTEIN-BINDING complex ;; HYDROLASE/PROTEIN-BINDING
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	38.34 Å
Radius of gyration Rg (electron density) rg_electron	38.39 Å
Forward intensity I(0) i0	183135000.00
Molecular weight molecular_weight	106090.0 kDa
Excluded volume excluded_volume	130920 Å³
Envelope volume envelope_volume	180180 Å³
Hydration-shell volume shell_volume	41689 Å³
Envelope diameter envelope_diameter	133.7 Å
Shell Rg shell_rg	41.04 Å
Envelope Rg envelope_rg	38.29 Å
Shape Rg shape_rg	38.38 Å
Total Rg total_rg	38.61 Å
Total atoms total_atoms	7272
Residues n_residues	845
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	134.8 Å
Rg (real space) rg_real	38.73 Å
Rg uncertainty (real space) rg_real_error	1.49 Å
I(0) (real space) i0_real	1.8310e+08
I(0) uncertainty (real space) i0_real_error	3.6460e+06
Rg (reciprocal space) rg_reciprocal	38.49 Å
I(0) (reciprocal space) i0_reciprocal	183100000.0000
Solution quality estimate total_estimate	0.7808
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.7 Å
Skewness Skewness skewness	0.554
Kurtosis Kurtosis kurtosis	-0.108
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15690000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.000

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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	19699.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	7542

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

Entity 2 Entity 2 polymer

Description description	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
Molecular weight formula_weight	7407.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MGEPTEFEYLRKVLFEYMMGRETKTMAKVITTVLKFPDDQTQKILEREDARLMSWLRSSS

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	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	270

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1upta_
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	d1uptb_
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	d1uptc_
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	d1uptd_
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	d1upte_
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	d1uptf_
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	d1uptg_
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	d1upth_
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	1uptA00
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	1uptB00
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	1uptC00
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	1uptD00
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	1uptE00
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	1uptF00
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	1uptG00
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	1uptH00
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	72.497 Å
Unit-cell length b length_b	89.711 Å
Unit-cell length c length_c	72.534 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	67.420 Å
R factor r_factor	0.2220
R_work r_work	0.2210
R_free r_free	0.2520

fit	/app/data/saxs_computation/up/1upt/1upt.fit
pddf	/app/data/pr_computation/up/1upt/1upt.pr.out
profile	/app/data/saxs_computation/up/1upt/1upt.dat

Structure of a complex of the golgin-245 GRIP domain 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

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)