4PAY

Crystal structure of an N-terminal fragment of the Legionella pneumophila effector protein SidC.

• PDB DOI: https://doi.org/10.2210/pdb4PAY/pdb
• Entry: 4PAY supersedes: 4OM6

• Classification: TRANSPORT PROTEIN
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-04-10 Released: 2014-06-25 
• Deposition Author(s): Horenkamp, F.A., Mukherjee, S., Alix, E., Schauder, C.M., Hubber, A.M., Roy, C.R., Reinisch, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Legionella pneumophila Subversion of Host Vesicular Transport by SidC Effector Proteins.

Horenkamp, F.A., Mukherjee, S., Alix, E., Schauder, C.M., Hubber, A.M., Roy, C.R., Reinisch, K.M.

(2014) Traffic 15: 488-499

• PubMed: 24483784 
• DOI: https://doi.org/10.1111/tra.12158
• Primary Citation of Related Structures:  
  4PAY


• PubMed Abstract: 
  

  Tethering proteins play a key role in vesicular transport, ensuring that cargo arrives at a specific destination. The bacterial effector protein SidC and its paralog SdcA have been described as tethering factors encoded by the intracellular pathogen Legionella pneumophila. Here, we demonstrate that SidC proteins are important for early events unique to maturation of vacuoles containing Legionella and discover monoubiquitination of Rab1 as a new SidC-dependent activity. The crystal structure of the SidC N-terminus revealed a novel fold that is important for function and could be involved in Legionella adaptations to evolutionarily divergent host cells it encounters in natural environments.

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Organizational Affiliation: 

Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.45 kDa 
• Atom Count: 9,616 
• Modelled Residue Count: 1,186 
• Deposited Residue Count: 1,220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SidC, interaptin	A, B	610	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: sidC, lpg2511
UniProt
Find proteins for Q5ZSK6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSK6  Go to UniProtKB:  Q5ZSK6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.46	α = 90
b = 107.584	β = 90
c = 177.538	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Horenkamp, F.A., Mukherjee, S., Alix, E., Schauder, C.M., Hubber, A.M., Roy, C.R., Reinisch, K.M.
• This entry supersedes: 4OM6

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy