3qbt

Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp

Method: X-RAY DIFFRACTION

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

Ras-related protein Rab-8A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Inositol polyphosphate 5-phosphatase OCRL-1 × 1 （Q01968） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Inositol polyphosphate 5-phosphatase OCRL-1 × 1 （Q01968） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Inositol polyphosphate 5-phosphatase OCRL-1 × 1 （Q01968） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Inositol polyphosphate 5-phosphatase OCRL-1 × 1 （Q01968） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB8A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–174； UniProt 6–176 Author chain C； PDBConstruct 4–174； UniProt 6–176 Author chain E； PDBConstruct 4–174； UniProt 6–176 Author chain G； PDBConstruct 4–174； UniProt 6–176

Inositol polyphosphate 5-phosphatase OCRL-1

Homo sapiens

UniProt Q01968

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-8A × 1 （P61006） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-8A × 1 （P61006） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-8A × 1 （P61006） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-8A × 1 （P61006） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OCRL_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–140； UniProt 540–678 Author chain D； PDBConstruct 2–140； UniProt 540–678 Author chain F； PDBConstruct 2–140； UniProt 540–678 Author chain H； PDBConstruct 2–140； UniProt 540–678

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	3qbt
Deposition date deposition_date	2011-01-14
Structure title title	Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
Keywords keywords	;Protein transport, vesicular trafficking, GTPase, Lowe syndrome, immunoglobulin fold, Rab8a, OCRL1, endocytosis, clathrin, APPL1, phosphoinositide, ASH, RhoGAP, PROTEIN TRANSPORT-HYDROLASE complex ;; PROTEIN TRANSPORT/HYDROLASE
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.

3qbt__assembly_1__model_1

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

Download this curve (.dat)

3qbt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qbt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.10 Å
Rg (electron density)	21.36 Å
Total Rg	22.17 Å
Atom count	2483
Residues	300
Excluded volume	44161 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qbt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3qbt__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3qbt__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3qbt__assembly_4__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rab-8A
Molecular weight formula_weight	20012.0 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	10400

GHMDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

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	Inositol polyphosphate 5-phosphatase OCRL-1
Molecular weight formula_weight	16554.7 kDa
EC 编号 ec_number	3.1.3.36
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

GERRYRKVFEDSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS

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	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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	308

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3qbta_
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	d3qbtc_
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	d3qbte_
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	d3qbtg_
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 (8 domains)

Domain ID domain_id	3qbtA00
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	3qbtB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qbtC00
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	3qbtD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qbtE00
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	3qbtF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qbtG00
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	3qbtH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	157.147 Å
Unit-cell length b length_b	55.340 Å
Unit-cell length c length_c	173.836 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	47.378 Å
R factor r_factor	0.2096
R_work r_work	0.2079
R_free r_free	0.2411

Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp

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

Ras-related protein Rab-8A

State in the Current Structure

Other States of the Same Protein in the Database

Inositol polyphosphate 5-phosphatase OCRL-1

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

3qbt__assembly_1__model_1

3qbt__assembly_1__model_1 | I(q)

3qbt__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp

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

Ras-related protein Rab-8A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inositol polyphosphate 5-phosphatase OCRL-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3qbt__assembly_1__model_1

3qbt__assembly_1__model_1 | I(q)

3qbt__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)