6CP2

SidC in complex with UbcH7~Ub


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into the ubiquitin transfer cascade catalyzed by theLegionellaeffector SidC.

Wasilko, D.J.Huang, Q.Mao, Y.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.36154
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The causative agent of Legionnaires' disease, <i>Legionella pneumophila </i>, delivers more than 330 virulent effectors to its host to establish an intracellular membrane-bound organelle called the <i>Legionella </i> containing vacuole. Among the a ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
SidC
A
542Legionella pneumophilaMutation(s): 1 
Find proteins for Q6RCR4 (Legionella pneumophila)
Go to UniProtKB:  Q6RCR4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 L3
B
154Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C
78Homo sapiensMutation(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 = 101.528α = 90.00
b = 101.528β = 90.00
c = 352.326γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5R01GM116964

Revision History 

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