7OPM | pdb_00007opm

Phosphorylated ERK2 in complex with ORF45


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.254 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7OPM

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host.

Alexa, A.Sok, P.Gross, F.Albert, K.Kobori, E.Poti, A.L.Gogl, G.Bento, I.Kuang, E.Taylor, S.S.Zhu, F.Ciliberto, A.Remenyi, A.

(2022) Nat Commun 13: 472-472

  • DOI: https://doi.org/10.1038/s41467-022-28109-x
  • Primary Citation Related Structures: 
    7OPM, 7OPO

  • PubMed Abstract: 

    The Kaposi's sarcoma associated herpesvirus protein ORF45 binds the extracellular signal-regulated kinase (ERK) and the p90 Ribosomal S6 kinase (RSK). ORF45 was shown to be a kinase activator in cells but a kinase inhibitor in vitro, and its effects on the ERK-RSK complex are unknown. Here, we demonstrate that ORF45 binds ERK and RSK using optimized linear binding motifs. The crystal structure of the ORF45-ERK2 complex shows how kinase docking motifs recognize the activated form of ERK. The crystal structure of the ORF45-RSK2 complex reveals an AGC kinase docking system, for which we provide evidence that it is functional in the host. We find that ORF45 manipulates ERK-RSK signaling by favoring the formation of a complex, in which activated kinases are better protected from phosphatases and docking motif-independent RSK substrate phosphorylation is selectively up-regulated. As such, our data suggest that ORF45 interferes with the natural design of kinase docking systems in the host.


  • Organizational Affiliation
    • Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary.

Macromolecule Content 

  • Total Structure Weight: 46.37 kDa 
  • Atom Count: 3,208 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 396 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1364Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
PHAROS:  P28482
GTEx:  ENSG00000100030 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
synthetic ERK2 inhibitor peptide18synthetic constructMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein ORF4514Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for F5HDE4 (Human herpesvirus 8 type P (isolate GK18))
Explore F5HDE4 
Go to UniProtKB:  F5HDE4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5HDE4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.094α = 90
b = 41.149β = 92.35
c = 51.701γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Development and Innovation Office (NKFIH)HungaryKKP 126963
European Union (EU)European UnioniNEXT Project 4788

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Data collection
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-31
    Changes: Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary