8K6F

LnaB-Actin-PRUb ternary complex

• PDB DOI: https://doi.org/10.2210/pdb8K6F/pdb

• Classification: TOXIN
• Organism(s): Oryctolagus cuniculus, Legionella, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-25 Released: 2025-01-29 
• Deposition Author(s): Chen, T.T., Ouyang, S.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Complex structure of Legionella effector LnaB with host Actin and PR-Ub

Chen, T.T., Ouyang, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 183.65 kDa 
• Atom Count: 12,703 
• Modelled Residue Count: 1,588 
• Deposited Residue Count: 1,606 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin gamma 1	A, B	375	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A8C6VAB1 (Naja naja) Explore A0A8C6VAB1  Go to UniProtKB:  A0A8C6VAB1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Legionella effector LnaB	C, D	352	Legionella	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	E, F	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	I [auth D]	[(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 C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
ATP (Subject of Investigation/LOI)	G [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.69	α = 90
b = 214.227	β = 90.3
c = 79.563	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Chen, T.T., Ouyang, S.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release