9RVP | pdb_00009rvp

Protein 2A from Theiler's murine encephalomyelitis virus (TMEV) bound to RNA pseudoknot

PDB DOI: https://doi.org/10.2210/pdb9RVP/pdb
NAKB: 9RVP

Classification: RNA
Organism(s): Theiler's encephalomyelitis virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-08 Released: 2025-07-30
Deposition Author(s): Betts, J.K., Jeffries, C.M., Passchier, T.C., Kung, H.C.Y., Graham, S.P., Abdelhamid, M.A.S., Howard, J.A.L., Craggs, T.D., Graham, S.C., Brierley, I., Leake, M.C., Quinn, S.D., Hill, C.H.
Funding Organization(s): Wellcome Trust, The Lister Institute of Preventive Medicine, Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC, United Kingdom), Engineering and Physical Sciences Research Council, iNEXT-Discovery, Alzheimers Research UK (ARUK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A new protein-dependent riboswitch activates ribosomal frameshifting

Betts, J.K., Jeffries, C.M., Passchier, T.C., Kung, H.C.Y., Graham, S.P., Abdelhamid, M.A., Howard, J.A.L., Craggs, T.D., Graham, S.C., Brierley, I., Leake, M.C., Quinn, S.D., Hill, C.H.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.07.17.665365

Macromolecule Content

Total Structure Weight: 26.8 kDa
Atom Count: 1,914
Modeled Residue Count: 153
Deposited Residue Count: 171
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	137	Theiler's encephalomyelitis virus	Mutation(s): 0
UniProt
Find proteins for B4YYP2 (Theiler's encephalomyelitis virus) Explore B4YYP2 Go to UniProtKB: B4YYP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4YYP2
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
RNA pseudoknot	B	34	Theiler's encephalomyelitis virus
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.191	α = 90
b = 45.931	β = 127.34
c = 65.72	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
xia2	data reduction
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	221818/Z/20/Z
The Lister Institute of Preventive Medicine	United Kingdom	--
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V000306/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/W006944/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T017805/1
Wellcome Trust	United Kingdom	098406/Z/12/B
Engineering and Physical Sciences Research Council	United Kingdom	EP/X525856/1
Engineering and Physical Sciences Research Council	United Kingdom	EP/V034030/1
Engineering and Physical Sciences Research Council	United Kingdom	EP/T518025/1
iNEXT-Discovery	European Union	871037
Alzheimers Research UK (ARUK)	United Kingdom	RF2019A-001