6yx5

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

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	Multifunctional virulence effector protein DrrA × 1 （Q29ST3） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 alpha-D-glucopyranose × 3 [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate × 1 SULFATE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1U7REJ8_MESAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–174； UniProt 6–176

Multifunctional virulence effector protein DrrA

Legionella pneumophila

UniProt Q29ST3

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 （A0A1U7REJ8） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 alpha-D-glucopyranose × 3 [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate × 1 SULFATE ION × 5 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–340； UniProt 16–352

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	6yx5
Deposition date deposition_date	2020-04-30
Structure title title	Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
Keywords keywords	vesicular trafficking virulence factor, CELL INVASION; CELL INVASION
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.

6yx5__assembly_1__model_1

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

Download this curve (.dat)

6yx5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yx5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.09 Å
Rg (electron density)	24.17 Å
Total Rg	25.04 Å
Atom count	4231
Residues	512
Excluded volume	75139 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yx5__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rab-8A
Molecular weight formula_weight	20042.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4353

SHMDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Multifunctional virulence effector protein DrrA
Molecular weight formula_weight	38837.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMFGSLYSDERDKPLLSPTAQKKFEEYQNKLANLSKIIRENEGNEVSPWQEWENGLRQIYKEMIYDAFDALGVEMPKDMEVHFAGSLAKAQATEYSDLDAFVIVKNDEDIKKVKPVFDALNNLCQRIFTASNQIYPDPIGINPSRLIGTPDDLFGMLKDGMVADVEATAMSILTSKPVLPRYECGEELRDKIKQEPSFSNMVSAKKFYNKAIKDFTAPKEGAEVVSVKTHIMRPIDFMLMGLREEFNLYSEDGAHLSAPGTIRLLREKNLLPEEQIARIESVYNQAMSKRFELHAEHKKEHDEMPYSDAKAMLDEVAKIRELGVQRVTRIENLENAKKL

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli BL21

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	1

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	1

Entity 5 Entity 5 non-polymer

Description description	alpha-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	[(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate
Molecular weight formula_weight	352.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6yx5a1
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	d6yx5a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	6yx5B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	6yx5B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1520 —

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Unit-cell length a length_a	142.309 Å
Unit-cell length b length_b	142.309 Å
Unit-cell length c length_c	76.616 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	48.060 Å
R factor r_factor	0.2084
R_work r_work	0.2068
R_free r_free	0.2385

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

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

Multifunctional virulence effector protein DrrA

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

6yx5__assembly_1__model_1

6yx5__assembly_1__model_1 | I(q)

6yx5__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6yx5__assembly_1__model_1

6yx5__assembly_1__model_1 | I(q)

6yx5__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)