1upt

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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4 × 2 （Q13439） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4 × 2 （Q13439） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1 × 2 （P40616） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1 × 2 （P40616） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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.

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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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1upt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1upt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1upt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.11 Å
Rg (electron density)	28.53 Å
Total Rg	29.15 Å
Atom count	3623
Residues	421
Excluded volume	65246 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1upt__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1upt__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1upt__assembly_1__model_1

1upt__assembly_1__model_1 | I(q)

1upt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1upt__assembly_1__model_1

1upt__assembly_1__model_1 | I(q)

1upt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)