6CP2

SidC in complex with UbcH7~Ub

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    6CP0, 6CP2

  • 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 ...

    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: 

    Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SidC A542Legionella pneumophilaMutation(s): 1 
Gene Names: C3927_12650
Find proteins for Q6RCR4 (Legionella pneumophila)
Explore Q6RCR4 
Go to UniProtKB:  Q6RCR4
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 L3 B154Homo sapiensMutation(s): 1 
Gene Names: UBE2L3, UBCE7, UBCH7
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Explore P68036 
Go to UniProtKB:  P68036
NIH Common Fund Data Resources
PHAROS:  P68036
GTEx:  ENSG00000185651
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B C78Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.528α = 90
b = 101.528β = 90
c = 352.326γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM116964

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence