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- PDB-7nbv: Structure of 2A protein from Theilers murine encephalomyelitis vi... -

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Basic information

Entry
Database: PDB / ID: 7nbv
TitleStructure of 2A protein from Theilers murine encephalomyelitis virus (TMEV)
ComponentsCapsid protein VP0
KeywordsVIRAL PROTEIN / TMEV / PRF / recoding / frameshifting / protein-mediated frameshifting / RNA-binding protein / translational regulation / ribosome-binding
Function / homology
Function and homology information


host cell nucleolus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity ...host cell nucleolus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / 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
BROMIDE ION / Genome polyprotein
Similarity search - Component
Biological speciesTheiler's murine encephalomyeltits virus GDVII
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsHill, C.H. / Cook, G.M. / Napthine, S. / Kibe, A. / Brown, K. / Caliskan, N. / Firth, A.E. / Graham, S.C. / Brierley, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202797/Z/16/Z United Kingdom
Wellcome Trust098406/Z/12/B United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus.
Authors: Hill, C.H. / Cook, G.M. / Napthine, S. / Kibe, A. / Brown, K. / Caliskan, N. / Firth, A.E. / Graham, S.C. / Brierley, I.
History
DepositionJan 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0452
Polymers15,9651
Non-polymers801
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, protein is monomeric in solution, as informed by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.788, 73.788, 73.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-377-

HOH

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Components

#1: Protein Capsid protein VP0 / Capsid protein VP1 / Capsid protein VP2 / Capsid protein VP3 / Capsid protein VP4 / Genome ...Capsid protein VP1 / Capsid protein VP2 / Capsid protein VP3 / Capsid protein VP4 / Genome polyprotein / Leader protein / P1A / P1B / P1C / P1D / Picornain 3C / Protease 3C / Protein 2C / Protein 3A / RNA-directed RNA polymerase / VP4-VP2 / VPg / Virion protein 1 / Virion protein 2 / Virion protein 3 / Virion protein 4 / protein 2B / 2A protein (derived from genome polyprotein)


Mass: 15965.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Theiler's murine encephalomyeltits virus GDVII
Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q88595, picornain 3C, RNA helicase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2A protein was concentrated to 4.38 mg/mL in 50 mM Tris (HCl) pH 7.4, 1.1 M NaCl, 1.0 mM DTT. 200 nL protein was mixed with 200 nL reservoir solution comprising 0.2 M KBr, 0.2 M potassium ...Details: 2A protein was concentrated to 4.38 mg/mL in 50 mM Tris (HCl) pH 7.4, 1.1 M NaCl, 1.0 mM DTT. 200 nL protein was mixed with 200 nL reservoir solution comprising 0.2 M KBr, 0.2 M potassium thiocyanate, 0.1 M sodium cacodylate pH 6.5, 3 % w/v poly-gamma-glutamic acid 200-400 and 10 % w/v PEG-MME 2000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationMonochromator: Si(111), single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.87→43.59 Å / Num. obs: 22710 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 26.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.026 / Net I/σ(I): 16.8
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 19.8 % / Rmerge(I) obs: 1.191 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1644 / CC1/2: 0.644 / Rpim(I) all: 0.273 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Cootmodel building
ARP/wARPmodel building
SHARPphasing
SHELXDphasing
Aimlessdata scaling
DIALSdata reduction
XDSdata reduction
xia2data reduction
GDAdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.87→42.6 Å / SU ML: 0.2357 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 1115 5.24 %
Rwork0.1847 20162 -
obs0.1872 21277 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.57 Å2
Refinement stepCycle: LAST / Resolution: 1.87→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 1 98 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531153
X-RAY DIFFRACTIONf_angle_d0.88961566
X-RAY DIFFRACTIONf_chiral_restr0.059161
X-RAY DIFFRACTIONf_plane_restr0.013200
X-RAY DIFFRACTIONf_dihedral_angle_d11.4178424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.960.39071580.34912442X-RAY DIFFRACTION96.73
1.96-2.060.35581260.29052539X-RAY DIFFRACTION98.7
2.06-2.190.30231060.25892532X-RAY DIFFRACTION98.99
2.19-2.360.27841390.21392522X-RAY DIFFRACTION99.29
2.36-2.590.27541570.22782499X-RAY DIFFRACTION99.51
2.59-2.970.27511240.20322564X-RAY DIFFRACTION99.67
2.97-3.740.20971220.15192549X-RAY DIFFRACTION100
3.74-42.60.15861830.12462515X-RAY DIFFRACTION99.96
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)
10.879962133961-0.3287013029470.6699110456222.27732654593-0.880358084290.8216357009240.1047020927620.177906517440.0405805107815-0.339027793715-0.0686191920902-0.1320032686350.2514279957540.0218377255322-0.009497998747790.180365275369-0.0014711988748-0.009276449926360.179076603431-0.01136030204710.17456955014792.1444787704-1.970913073850.5771082593
21.969052427240.159166735569-1.369562942791.4731673601-0.2745894043231.36162783116-0.07024550651570.210818491572-0.0591380826073-0.09060249980540.06798557811720.06757150712340.128778179988-0.219181662135-0.00256265130250.195857671427-0.00551582452275-0.02268577345630.253496803202-0.01201875371780.19907540502284.380780237-0.36315452900653.5144288534
32.6142409327-0.23953786392-1.337059002111.632414749311.112474696463.62448162499-0.02771457320810.255472111049-0.0736817640427-0.18120224735-0.1245883844880.238459180834-0.310888767493-0.501318752540.1410765716350.2498990983240.0476827817131-0.05535835922810.2918102416710.008205528667220.22791301642983.511716605310.424463832446.9657557179
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -4 through 17 )-4 - 171 - 22
22chain 'A' and (resid 18 through 104 )18 - 10423 - 109
33chain 'A' and (resid 105 through 126 )105 - 126110 - 131

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