Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 88880.47 
• Atom Count: 5928 
• Residue Count: 774 
• Unique protein chains: 3

6CP2

SidC in complex with UbcH7~Ub

• DOI: 10.2210/pdb6CP2/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2018-03-13 Released: 2018-08-01 
• Deposition Author(s): Wasilko, D.J., Huang, Q., Mao, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.288 
• R-Value Work: 0.210 

Literature

Insights into the ubiquitin transfer cascade catalyzed by theLegionellaeffector SidC.

Wasilko, D.J., Huang, Q., Mao, Y.

(2018) Elife 7: --

• PubMed: 30015617 
• DOI: 10.7554/eLife.36154
• Primary Citation of Related Structures:  
  6CP0


• PubMed Abstract: 
  

The causative agent of Legionnaires' disease, Legionella pneumophila , delivers more than 330 virulent effectors to its host to establish an intracellular membrane-bound organelle called the Legionella containing vacuole. Among the army of Legionella effectors, SidC and its paralog SdcA have been identified as novel bacterial ubiquitin (Ub) E3 ligases. To gain insight into the molecular mechanism of SidC/SdcA as Ub ligases, we determined the crystal structures of a binary complex of the N-terminal catalytic SNL domain of SdcA with its cognate E2 UbcH5C and a ternary complex consisting of the SNL domain of SidC with the Ub-linked E2 UbcH7. These two structures reveal the molecular determinants governing the Ub transfer cascade catalyzed by SidC. Together, our data support a common mechanism in the Ub transfer cascade in which the donor Ub is immobilized with its C-terminal tail locked in an extended conformation, priming the donor Ub for catalysis.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States.,MacCHESS, Cornell University, Ithaca, United States.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SidC	A	542	Legionella pneumophila	Mutation(s): 1
Find proteins for Q6RCR4 (Legionella pneumophila) Go to UniProtKB:  Q6RCR4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 L3	B	154	Homo sapiens	Mutation(s): 1  Gene Names: UBE2L3 (UBCE7, UBCH7) EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens) Go to Gene View: UBE2L3 Go to UniProtKB:  P68036

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	C	78	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.288 
• R-Value Work: 0.210 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 101.528	α = 90.00
b = 101.528	β = 90.00
c = 352.326	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-13 
• Released Date: 2018-08-01 
• Deposition Author(s): Wasilko, D.J., Huang, Q., Mao, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	5R01GM116964

Revision History 

• Version 1.0: 2018-08-01
  Type: Initial release
• Version 1.1: 2019-02-20
  Type: Author supporting evidence, Data collection