7BNY | pdb_00007bny

Structure of 2A protein from encephalomyocarditis virus (EMCV)

PDB DOI: https://doi.org/10.2210/pdb7BNY/pdb

Classification: VIRAL PROTEIN
Organism(s): Mengo virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-22 Released: 2021-12-08
Deposition Author(s): Hill, C.H., Napthine, S., Pekarek, L., Kibe, A., Firth, A.E., Graham, S.C., Caliskan, N., Brierley, I.
Funding Organization(s): Wellcome Trust, European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch.

Hill, C.H., Pekarek, L., Napthine, S., Kibe, A., Firth, A.E., Graham, S.C., Caliskan, N., Brierley, I.

(2021) Nat Commun 12: 7166-7166

PubMed: 34887415 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27400-7
Primary Citation Related Structures:
7BNY

PubMed Abstract:
Programmed -1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection.

Organizational Affiliation

Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. chris.hill@york.ac.uk.

Macromolecule Content

Total Structure Weight: 72.19 kDa
Atom Count: 4,596
Modeled Residue Count: 524
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B, C, D	152	Mengo virus	Mutation(s): 0 EC: 3.6.4.13 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P12296 (Mengo encephalomyocarditis virus) Explore P12296 Go to UniProtKB: P12296
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12296
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth D], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.225 (Depositor), 0.225 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.56	α = 90
b = 91.56	β = 90
c = 316.39	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
xia2	data reduction
XDS	data reduction
Aimless	data scaling
SHARP	phasing
SHELXD	phasing
PHENIX	refinement
ARP/wARP	model building
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202797/Z/16/Z
Wellcome Trust	United Kingdom	098406/Z/12/B
European Communitys Seventh Framework Programme	European Union	BIOSTRUCT-X (Contract No. 283570)