7LMS

Structure of human SetD3 methyl-transferase in complex with 2A protease from Coxsackievirus B3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3.

Peters, C.E.Schulze-Gahmen, U.Eckhardt, M.Jang, G.M.Xu, J.Pulido, E.H.Bardine, C.Craik, C.S.Ott, M.Gozani, O.Verba, K.A.Huttenhain, R.Carette, J.E.Krogan, N.J.

(2022) Nat Commun 13: 5282-5282

  • DOI: https://doi.org/10.1038/s41467-022-32758-3
  • Primary Citation of Related Structures:  
    7LMS

  • PubMed Abstract: 

    Enteroviruses cause a number of medically relevant and widespread human diseases with no approved antiviral therapies currently available. Host-directed therapies present an enticing option for this diverse genus of viruses. We have previously identified the actin histidine methyltransferase SETD3 as a critical host factor physically interacting with the viral protease 2A. Here, we report the 3.5 Å cryo-EM structure of SETD3 interacting with coxsackievirus B3 2A at two distinct interfaces, including the substrate-binding surface within the SET domain. Structure-function analysis revealed that mutations of key residues in the SET domain resulted in severely reduced binding to 2A and complete protection from enteroviral infection. Our findings provide insight into the molecular basis of the SETD3-2A interaction and a framework for the rational design of host-directed therapeutics against enteroviruses.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease 2AA [auth B]151Coxsackievirus B3 (strain Nancy)Mutation(s): 1 
EC: 3.4.22.29
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03313
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-histidine N-methyltransferaseB [auth A]596Homo sapiensMutation(s): 0 
Gene Names: SETD3C14orf154
EC: 2.1.1.85
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TU7 (Homo sapiens)
Explore Q86TU7 
Go to UniProtKB:  Q86TU7
PHAROS:  Q86TU7
GTEx:  ENSG00000183576 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86TU7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.14
MODEL REFINEMENTRosetta3
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTISOLDE1.01
MODEL REFINEMENTRosetta3
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTISOLDE1.01

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references, Refinement description