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- PDB-6gvy: Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mout... -

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Basic information

Entry
Database: PDB / ID: 6gvy
TitleMutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus complexed with an template -primer RNA
Components
  • Genome polyprotein
  • RNA (5'-R(P*CP*CP*GP*GP*G)-3')
  • RNA (5'-R(P*CP*UP*CP*CP*CP*GP*GP*G)-3')
KeywordsVIRAL PROTEIN / RNA dependent RNA polymerase / Picornavirus / closed right hand conformation
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / 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. / Alpha-Beta Plaits / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type C
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2014-54588- Spain
Spanish Ministry of Economy and CompetitivenessMaria de Maeztu Unit of Excellence MDM-2014-0435 Spain
CitationJournal: J. Virol. / Year: 2018
Title: Contribution of a Multifunctional Polymerase Region of Foot-and-Mouth Disease Virus to Lethal Mutagenesis.
Authors: de la Higuera, I. / Ferrer-Orta, C. / Moreno, E. / de Avila, A.I. / Soria, M.E. / Singh, K. / Caridi, F. / Sobrino, F. / Sarafianos, S.G. / Perales, C. / Verdaguer, N. / Domingo, E.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: RNA (5'-R(P*CP*CP*GP*GP*G)-3')
C: RNA (5'-R(P*CP*UP*CP*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2614
Polymers58,1693
Non-polymers921
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-33 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.073, 94.073, 99.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Genome polyprotein


Mass: 54050.219 Da / Num. of mol.: 1 / Mutation: M16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type C / Production host: Escherichia coli (E. coli) / References: UniProt: Q0QEE0, UniProt: P03311*PLUS
#2: RNA chain RNA (5'-R(P*CP*CP*GP*GP*G)-3')


Mass: 1601.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*CP*UP*CP*CP*CP*GP*GP*G)-3')


Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M MES[2-(N-morpholino) ethanesulfonic acid] pH 6.0 and 4% butyrolactone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26375 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Num. unique all: 3774

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wne

1wne


Resolution: 2.2→42.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.746 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27425 1349 5.1 %RANDOM
Rwork0.2328 ---
obs0.23484 24864 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.444 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å2-0 Å2
2---0.16 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.2→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 258 6 42 4031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0144105
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173510
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.6235616
X-RAY DIFFRACTIONr_angle_other_deg0.781.6858214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13121.691207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14615623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0281527
X-RAY DIFFRACTIONr_chiral_restr0.0460.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3064.8661899
X-RAY DIFFRACTIONr_mcbond_other1.3064.8631898
X-RAY DIFFRACTIONr_mcangle_it2.2257.2922372
X-RAY DIFFRACTIONr_mcangle_other2.2257.2962373
X-RAY DIFFRACTIONr_scbond_it1.1565.1542206
X-RAY DIFFRACTIONr_scbond_other1.1555.1542206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.947.7083245
X-RAY DIFFRACTIONr_long_range_B_refined4.02656.5484597
X-RAY DIFFRACTIONr_long_range_B_other4.02556.5554598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.567 75 -
Rwork0.514 1699 -
obs--93.61 %
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)
10.3316-0.08160.40312.1414-0.4510.8769-0.0806-0.01630.0339-0.150.0866-0.07920.1079-0.1471-0.0060.1456-0.0007-0.03740.1912-0.01150.020318.478426.495823.9383
24.3706-4.3498-2.24287.67677.724210.1618-0.3231-0.4263-0.10150.27610.43180.0080.09070.2211-0.10870.03080.03640.02780.16130.1070.134314.93636.648223.8513
30.0083-0.001-0.00970.0025-0.0020.0173-0.03080.01070.0010.01430.0168-0.00010.0243-0.03780.0140.1630.03780.01540.1507-0.01020.121714.08134.503430.1702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 475
2X-RAY DIFFRACTION2B916 - 920
3X-RAY DIFFRACTION3C904 - 910

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