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- PDB-9rvp: Protein 2A from Theiler's murine encephalomyelitis virus (TMEV) b... -

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Basic information

Entry
Database: PDB / ID: 9rvp
TitleProtein 2A from Theiler's murine encephalomyelitis virus (TMEV) bound to RNA pseudoknot
Components
  • Genome polyprotein
  • RNA pseudoknot
KeywordsRNA / pseudoknot / RNA-protein complex / frameshifting / cardiovirus
Function / homology
Function and homology information


host cell nucleolus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...host cell nucleolus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid ...Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesTheiler's encephalomyelitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBetts, 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. ...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 support United Kingdom, European Union, 11items
OrganizationGrant numberCountry
Wellcome Trust221818/Z/20/Z United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V000306/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W006944/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T017805/1 United Kingdom
Wellcome Trust098406/Z/12/B United Kingdom
Engineering and Physical Sciences Research CouncilEP/X525856/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/V034030/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/T518025/1 United Kingdom
iNEXT-Discovery871037European Union
Alzheimers Research UK (ARUK)RF2019A-001 United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: A new protein-dependent riboswitch activates ribosomal frameshifting
Authors: 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.
History
DepositionJul 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: RNA pseudoknot


Theoretical massNumber of molelcules
Total (without water)26,8012
Polymers26,8012
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.191, 45.931, 65.720
Angle α, β, γ (deg.)90.000, 127.340, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-327-

HOH

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Components

#1: Protein Genome polyprotein


Mass: 15967.319 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension GSHM... is due to TEV cleavage of an N-terminal His6-MBP tag. C-terminal ...VEMNPG residues were disordered and could not be modelled.
Source: (gene. exp.) Theiler's encephalomyelitis virus / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q88595
#2: RNA chain RNA pseudoknot


Mass: 10833.512 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: UAA in pseudoknot loop 2 is disordered and could not be modelled. Density for the 3' C was insufficient for modelling.
Source: (synth.) Theiler's encephalomyelitis virus / References: GenBank: M20301.1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.3 % / Description: needles, required dissection
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 150 nL 2A-RNA complex (7.5 mg/mL, 693 uM) in 10 mM HEPES pH 7.4, 100 mM NaCl, 1 mM MgCl2, 1 mM DTT was mixed with 150 nL 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.9, 19% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 10, 2024
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→52.25 Å / Num. obs: 19441 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.065 / Rrim(I) all: 0.166 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1235 / CC1/2: 0.64 / Rpim(I) all: 0.308 / Rrim(I) all: 0.792 / % possible all: 98.3

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Processing

Software
NameVersionClassification
GDAdata collection
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→52.25 Å / SU ML: 0.3061 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 894 4.61 %
Rwork0.1931 18516 -
obs0.1948 19410 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→52.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 635 0 249 1914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941771
X-RAY DIFFRACTIONf_angle_d0.83132533
X-RAY DIFFRACTIONf_chiral_restr0.0547299
X-RAY DIFFRACTIONf_plane_restr0.0124209
X-RAY DIFFRACTIONf_dihedral_angle_d13.3552739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.34091640.32423011X-RAY DIFFRACTION97.78
2.02-2.170.32391540.29123050X-RAY DIFFRACTION97.8
2.18-2.390.28821550.24633033X-RAY DIFFRACTION98.46
2.39-2.740.26131450.19643086X-RAY DIFFRACTION98.75
2.74-3.450.2021510.16053125X-RAY DIFFRACTION99.39
3.45-52.250.15421250.14253211X-RAY DIFFRACTION99.37
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.77543303158-1.3432683180.2481773450553.857468376790.789425692592.743560726520.09468697714370.0399827579810.0883598356561-0.0511985500459-0.2245607441840.230609289104-0.190156109179-0.1694244063240.1180221663040.154158744387-0.0325511498952-0.008268808248960.07727212688790.01333808925120.1281381318164.061512511755.1540865523812.0678291214
22.53196600791-0.9818124126130.4818071088694.98650074602-1.920463607542.4856950699-0.0752847620397-0.2711032704030.08693544591410.6224066554290.0193838631241-0.118319399896-0.265415544010.1025757214220.01802787136530.196879533126-0.00165859961398-0.008481848556440.12656851829-0.01924229551420.12712828291112.02864829626.5069297456723.4986407235
34.04126914073-0.198343762642.557270128391.32294118053-0.5290174494786.073882759970.21425098846-0.0133176385209-0.225738285113-0.18940302273-0.0690124192822-0.02298047666620.680733998157-0.104486079635-0.1092966232740.1971657104680.00536058530225-0.003005670673340.09341179638570.01262899735750.1360346617425.75862264389-6.4526413157413.8221836418
44.737628473550.419315458379-0.7006280128664.225511356532.169184469687.39030523574-0.0103255911212-0.3105799816660.480153736255-0.232053338568-0.1441135592720.177697964509-0.754034880813-0.290576772320.02989955262770.394711411717-0.03412487349480.07161293848670.2044203315460.02831881320010.32761432604715.076616036622.915996547514.2018558667
55.16736727390.481533257278-6.051715793530.0477085615659-0.5537470140417.15084253018-0.3098562669070.808440245267-0.425707165095-0.0174500472540.01801068364110.08221444118560.355629996546-0.7990789708740.3168355357380.2596747612370.00975612266205-0.01285545555120.2141507514570.009440239484760.25499228711528.53791810077.98283702844-3.85439745098
64.434300538153.80027335162-2.413554711293.40415320541-1.770282065761.886355280350.516897076816-0.3917263409380.8227468437880.360459296854-0.4653951772410.379422795935-1.231835305662.079590472680.09028585206660.499824124808-0.382411048898-0.08408224051960.7493648116870.10389632510.4169503192830.263539864314.108089593211.9979970066
73.164233188240.407656188696-2.611574335022.58420753511-2.143363952913.42260854019-0.011743560540.239313848685-0.40089192473-0.3876775438380.01277092265780.2623220811140.251409632525-0.299225407661-0.09399106926550.195476668592-0.07163474421680.005757993040640.184471004858-0.02458675393380.39145272283327.905965248511.0458487141-5.45727099623
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 63 )AA5 - 631 - 59
22chain 'A' and (resid 64 through 104 )AA64 - 10460 - 100
33chain 'A' and (resid 105 through 127 )AA105 - 127101 - 123
44chain 'B' and (resid 14 through 18 )BB14 - 18
55chain 'B' and (resid 19 through 28 )BB19 - 28
66chain 'B' and (resid 29 through 36 )BB29 - 36
77chain 'B' and (resid 37 through 46 )BB37 - 46

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