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6yx5

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

Method: X-RAY DIFFRACTION Dmax: 80.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ras-related protein Rab-8A

Homo sapiens

UniProt A0A1U7REJ8

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 6–176 Not recorded Multifunctional virulence effector protein DrrA × 1 （Q29ST3） MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 GLC alpha-D-glucopyranose × 3 LJN [(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 SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1M bicine, pH 9, 2.4M ammonium sulphate Resolution 2.14 Å R-free 0.238

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.

No other PDB entry for the same UniProt protein was found.

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 16–352 Not recorded Ras-related protein Rab-8A × 1 （A0A1U7REJ8） MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 GLC alpha-D-glucopyranose × 3 LJN [(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 SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.1M bicine, pH 9, 2.4M ammonium sulphate Resolution 2.14 Å R-free 0.238

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 6YX5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2WWX Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex Deposited 2009-10-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 317–533（217 aa） Fragment：RESIDUES 317-533
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.231
3L0I Complex structure of SidM/DrrA with the wild type Rab1 Deposited 2009-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 193–550（358 aa） Fragment：GEF/GDF domain, residues 193-550
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.266
3L0I Complex structure of SidM/DrrA with the wild type Rab1 Deposited 2009-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 193–550（358 aa） Fragment：GEF/GDF domain, residues 193-550
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.85 Å R-free 0.266
3L0M Crystal structure of Rab1-activation domain and P4M domain of SidM/DrrA from legionella Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 317–647（331 aa） Fragment：Rab1-activation domain, P4M domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.6M potassium sodium tartrate, 0.1M CHES, 0.1M Li2SO4, 0.1M sodium acetate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.45 Å R-free 0.241
3L0M Crystal structure of Rab1-activation domain and P4M domain of SidM/DrrA from legionella Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 317–647（331 aa） Fragment：Rab1-activation domain, P4M domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.6M potassium sodium tartrate, 0.1M CHES, 0.1M Li2SO4, 0.1M sodium acetate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.45 Å R-free 0.241
3NKU Crystal structure of the N-terminal domain of DrrA/SidM from Legionella pneumophila Deposited 2010-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 9–218（210 aa） Fragment：N-terminal domain (residues 9-218)
Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；35 - 40% (v/v) PEG600, 0.1 M phosphate/citrate, 3% (w/v) glucose monohydrate, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.10 Å R-free 0.228
3NKU Crystal structure of the N-terminal domain of DrrA/SidM from Legionella pneumophila Deposited 2010-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 9–218（210 aa） Fragment：N-terminal domain (residues 9-218)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；35 - 40% (v/v) PEG600, 0.1 M phosphate/citrate, 3% (w/v) glucose monohydrate, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.10 Å R-free 0.228
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 340–533（194 aa）
Mutation：D512C GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 340–533（194 aa）
Mutation：D512C GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 340–533（194 aa）
Mutation：D512C GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 340–533（194 aa）
Mutation：D512C GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 340–533（194 aa）
Mutation：D512C GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 340–533（194 aa）
Mutation：D512C GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Resolution 2.50 Å R-free 0.266

5 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6yx5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6yx5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6yx5
Deposition date deposition_date2020-04-30
Structure title titleStructure of DrrA from Legionella pneumophilia in complex with human Rab8a
Keywords keywordsvesicular trafficking virulence factor, CELL INVASION; CELL INVASION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.09 Å
Radius of gyration Rg (electron density) rg_electron24.17 Å
Forward intensity I(0) i063097600.00
Molecular weight molecular_weight60489.0 kDa
Excluded volume excluded_volume75139 ų
Envelope volume envelope_volume90506 ų
Hydration-shell volume shell_volume30668 ų
Envelope diameter envelope_diameter89.3 Å
Shell Rg shell_rg31.88 Å
Envelope Rg envelope_rg24.59 Å
Shape Rg shape_rg24.15 Å
Total Rg total_rg25.04 Å
Total atoms total_atoms4231
Residues n_residues512
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax80.9 Å
Rg (real space) rg_real24.99 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real6.3100e+07
I(0) uncertainty (real space) i0_real_error6.7800e+05
Rg (reciprocal space) rg_reciprocal25.02 Å
I(0) (reciprocal space) i0_reciprocal63100000.0000
Solution quality estimate total_estimate0.8951
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8 Å
Skewness Skewness skewness0.202
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11920000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.975
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6yx5a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd6yx5a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id6yx5B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily170 —
Domain ID domain_id6yx5B02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1520 —
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8. Citations (1)

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9. Files and Curves (10)