8XEP

Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb8XEP/pdb

• Classification: HYDROLASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-12-12 Released: 2024-05-01 
• Deposition Author(s): Tan, J.X., Wang, X.F., Zhou, Y., Zhu, Y.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin

Tan, J.X., Wang, X.F., Zhou, Y., Zhu, Y.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 118.88 kDa 
• Atom Count: 6,924 
• Modelled Residue Count: 883 
• Deposited Residue Count: 1,062 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV effector MavL	A, D	455	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 1  Gene Names: lpg2526
UniProt
Find proteins for Q5ZSJ1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSJ1  Go to UniProtKB:  Q5ZSJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth A], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.951	α = 90
b = 56.696	β = 90
c = 100.238	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Tan, J.X., Wang, X.F., Zhou, Y., Zhu, Y.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81925024
Ministry of Science and Technology (MoST, China)	China	2017YFA0503900

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release