5o74

Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP

Method: X-RAY DIFFRACTION

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

Multifunctional virulence effector protein DrrA

Legionella pneumophila

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-1B × 1 （Q9H0U4） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1B × 1 （Q9H0U4） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1B × 1 （Q9H0U4） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1B × 1 （Q9H0U4） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1B × 1 （Q9H0U4） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1B × 1 （Q9H0U4） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DRRA_LEGPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–197； UniProt 340–533 Author chain C； PDBConstruct 4–197； UniProt 340–533 Author chain E； PDBConstruct 4–197； UniProt 340–533 Author chain G； PDBConstruct 4–197； UniProt 340–533 Author chain I； PDBConstruct 4–197； UniProt 340–533 Author chain K； PDBConstruct 4–197； UniProt 340–533

Ras-related protein Rab-1B

Homo sapiens

UniProt Q9H0U4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB1B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–174； UniProt 3–174 Author chain D； PDBConstruct 3–174； UniProt 3–174 Author chain F； PDBConstruct 3–174； UniProt 3–174 Author chain H； PDBConstruct 3–174； UniProt 3–174 Author chain J； PDBConstruct 3–174； UniProt 3–174 Author chain L； PDBConstruct 3–174； UniProt 3–174

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	5o74
Deposition date deposition_date	2017-06-08
Structure title title	Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP
Keywords keywords	Rab1b, DrrA, exchange factor, Legionella pneumophila, hydrolase; 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.

5o74__assembly_1__model_1

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

Download this curve (.dat)

5o74__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5o74__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.83 Å
Rg (electron density)	20.74 Å
Total Rg	21.64 Å
Atom count	5752
Residues	360
Excluded volume	51442 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5o74__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5o74__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5o74__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5o74__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5o74__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5o74__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Description description	Multifunctional virulence effector protein DrrA
Molecular weight formula_weight	22001.2 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	D512C
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	33987

GHMVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNCETLESVLSSKGENLSEYLSYK

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-1B
Molecular weight formula_weight	20605.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

MAPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYXGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGHHHHHH

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'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	man
Copy count entity_count	6

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

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5o74b_
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	d5o74d_
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	d5o74f_
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	d5o74h_
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	d5o74j_
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	d5o74l_
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 (12 domains)

Domain ID domain_id	5o74A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5o74B00
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	5o74C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5o74D00
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	5o74E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5o74F00
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	5o74G00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5o74H00
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	5o74I00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5o74J00
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	5o74K00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	5o74L00
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

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Unit-cell length a length_a	77.910 Å
Unit-cell length b length_b	87.450 Å
Unit-cell length c length_c	93.170 Å
Unit-cell angle α angle_alpha	114.61 °
Unit-cell angle β angle_beta	97.69 °
Unit-cell angle γ angle_gamma	100.74 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	46.525 Å
R factor r_factor	0.2304
R_work r_work	0.2286
R_free r_free	0.2660

Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP

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

Multifunctional virulence effector protein DrrA

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-1B

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

5o74__assembly_1__model_1

5o74__assembly_1__model_1 | I(q)

5o74__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Source Source

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP

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

Multifunctional virulence effector protein DrrA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related protein Rab-1B

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

5o74__assembly_1__model_1

5o74__assembly_1__model_1 | I(q)

5o74__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Source Source

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)