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8j9b

LnaB-actin binary complex

Method: X-RAY DIFFRACTION Dmax: 193.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin gamma 1

OrganismNot specified

UniProt A0A8C6VAB1

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 × 20 PDB declaration: 20-meric（20） Consistent with protein copy count Chain A； UniProt 1–375 Chain B； UniProt 1–375 Chain C； UniProt 1–375 Chain D； UniProt 1–375 Chain E； UniProt 1–375 Chain F； UniProt 1–375 Not recorded Type IV secretion protein Dot × 8 （A0AA44XJB8） X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；289 K；PEG4000,Sodium HEPES,Ammonnium sulfate Resolution 3.42 Å R-free 0.298

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 8J9B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8K6E LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–375（375 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG 8000; Sodium chloride; Sodium HEPES
Resolution 2.74 Å R-free 0.245
8K6F LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–375（375 aa）
Chain B 1–375（375 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG8000, Sodium Choride, Sodium HEPES
Resolution 3.41 Å R-free 0.243
8K6I LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–375（375 aa）
Chain B 1–375（375 aa）
Not recorded PO4 PHOSPHATE ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Sodium Chloride, PEG8000, HEPES
Resolution 3.19 Å R-free 0.315
8K6R LnaB-Actin-PRUb ternary complex in the presence of AMPPNP Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–375（375 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Sodium Chloride, Sodium HEPES, PEG8000
Resolution 2.76 Å R-free 0.261
8K6V LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–375（375 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Magnesium acetate, MOPS, PEG8000
Resolution 2.60 Å R-free 0.307

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

View Construct and Data Evidence
UniProt name A0A8C6VAB1_NAJNA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–375； UniProt 1–375 Author chain B； PDBConstruct 1–375； UniProt 1–375 Author chain C； PDBConstruct 1–375； UniProt 1–375 Author chain D； PDBConstruct 1–375； UniProt 1–375 Author chain E； PDBConstruct 1–375； UniProt 1–375 Author chain F； PDBConstruct 1–375； UniProt 1–375

Type IV secretion protein Dot

Legionella pneumophila

UniProt A0AA44XJB8

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 × 20 PDB declaration: 20-meric（20） Consistent with protein copy count Chain H； UniProt 1–441 Chain I； UniProt 1–441 Chain J； UniProt 1–441 Chain K； UniProt 1–441 Not recorded Actin gamma 1 × 12 （A0A8C6VAB1） X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；289 K；PEG4000,Sodium HEPES,Ammonnium sulfate Resolution 3.42 Å R-free 0.298

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 A0AA44XJB8_LEGPN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain H； PDBConstruct 1–441； UniProt 1–441 Author chain I； PDBConstruct 1–441； UniProt 1–441 Author chain J； PDBConstruct 1–441； UniProt 1–441 Author chain K； PDBConstruct 1–441； UniProt 1–441

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 8j9b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8j9b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8j9b
Deposition date deposition_date2023-05-03
Structure title titleLnaB-actin binary complex
Keywords keywordsLegionella, AMPylation, Actin, TRANSFERASE; TRANSFERASE
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_guinier63.85 Å
Radius of gyration Rg (electron density) rg_electron63.14 Å
Forward intensity I(0) i01972960000.00
Molecular weight molecular_weight381020.0 kDa
Excluded volume excluded_volume479110 ų
Envelope volume envelope_volume800210 ų
Hydration-shell volume shell_volume104640 ų
Envelope diameter envelope_diameter188.2 Å
Shell Rg shell_rg69.43 Å
Envelope Rg envelope_rg58.91 Å
Shape Rg shape_rg63.16 Å
Total Rg total_rg63.20 Å
Total atoms total_atoms26804
Residues n_residues3374
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 dmax193.3 Å
Rg (real space) rg_real63.28 Å
Rg uncertainty (real space) rg_real_error1.36 Å
I(0) (real space) i0_real1.9730e+09
I(0) uncertainty (real space) i0_real_error3.8360e+07
Rg (reciprocal space) rg_reciprocal64.30 Å
I(0) (reciprocal space) i0_reciprocal1976000000.0000
Solution quality estimate total_estimate0.8197
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary92.8 Å
Skewness Skewness skewness-0.141
Kurtosis Kurtosis kurtosis-0.588
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha58760000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)