8K6E | pdb_00008k6e

LnaB-Actin-PRUb ternary complex

• PDB DOI: https://doi.org/10.2210/pdb8K6E/pdb

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


• Deposited: 2023-07-25 Released: 2025-02-05 
• 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: 2.74 Å
• R-Value Free: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.191 (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 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 92.05 kDa 
• Atom Count: 6,404 
• Modeled Residue Count: 789 
• Deposited Residue Count: 802 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin gamma 1	A	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	B	352	Legionella	Mutation(s): 0
UniProt
Find proteins for Q5ZSJ0 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSJ0  Go to UniProtKB:  Q5ZSJ0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	C	75	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	E [auth C]	[(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
ANP (Subject of Investigation/LOI)	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.317	α = 90
b = 55.152	β = 90
c = 80.907	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: 2025-02-05 
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: 2025-02-05
  Type: Initial release