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- PDB-3nl0: Mutant P44S M296I of Foot-and-mouth disease Virus RNA-dependent R... -

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Basic information

Entry
Database: PDB / ID: 3nl0
TitleMutant P44S M296I of Foot-and-mouth disease Virus RNA-dependent RNA polymerase
Components
  • 3D polymerase
  • 5'-R(*G*GP*GP*CP*CP*C)-3'
  • 5'-R(P*UP*GP*GP*GP*CP*CP*C)-3'
KeywordsTRANSFERASE/RNA / Foot-and-mouth disease Virus Picornavirus / 3D polymerase / RNA dependent RNA polymerase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / 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 / Alpha-Beta Plaits / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAgudo, R. / Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Verdaguer, N. / Domingo, E.
CitationJournal: Plos Pathog. / Year: 2010
Title: A multi-step process of viral adaptation to a mutagenic nucleoside analogue by modulation of transition types leads to extinction-escape.
Authors: Agudo, R. / Ferrer-Orta, C. / Arias, A. / de la Higuera, I. / Perales, C. / Perez-Luque, R. / Verdaguer, N. / Domingo, E.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,4305
Polymers57,3813
Non-polymers492
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-33 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.713, 93.713, 99.723
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 3D polymerase


Mass: 53262.426 Da / Num. of mol.: 1 / Mutation: P44S, M296I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type C / Strain: C-S8c1 / Gene: 3D / Plasmid: pET28a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9QCE4
#2: RNA chain 5'-R(P*UP*GP*GP*GP*CP*CP*C)-3'


Mass: 2212.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetize
#3: RNA chain 5'-R(*G*GP*GP*CP*CP*C)-3'


Mass: 1906.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetize
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 35% PEG 4000, 0.2M sodium acetate, 0.1M sodium citrate, 4% butyrolactone , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 8, 2008
RadiationMonochromator: diamond monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 15946 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.8

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Processing

Software
NameClassification
MxCuBEdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNE

1wne


Resolution: 2.6→29.32 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 29.369 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27412 794 5 %RANDOM
Rwork0.2263 ---
obs0.22867 15092 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.039 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å20 Å2
2--1.41 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 272 2 40 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8512.0335629
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3455474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3623.315178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1115623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9731527
X-RAY DIFFRACTIONr_chiral_restr0.0550.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213061
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2141.52359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.40723790
X-RAY DIFFRACTIONr_scbond_it0.43331753
X-RAY DIFFRACTIONr_scangle_it0.7084.51839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 50 -
Rwork0.253 1075 -
obs--96.82 %
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)
10.8175-0.13790.42112.9178-0.57631.3741-0.10230.04070.1104-0.32570.1317-0.01610.1214-0.1821-0.02930.23450.04070.01840.2779-0.04180.155418.655226.442223.8653
223.1556-9.8656-3.04149.1831-7.500115.9397-3.0886-2.8408-0.26080.9513.52210.34290.9903-3.7769-0.43350.66130.22310.06421.48290.08670.166514.50434.041230.1918
329.8851-29.95678.142243.96859.983225.8504-1.0947-0.1062-0.6737-0.5182-0.78762.2212-2.3857-1.2561.88230.3067-0.0044-0.05580.23-0.24730.317113.224838.171724.8792
40.5005-0.55680.18542.72330.06630.4912-0.16970.04120.0524-0.16590.1606-0.21710.2039-0.06450.00910.4015-0.03740.00760.34540.01250.130419.591120.117429.5677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 475
2X-RAY DIFFRACTION2B904 - 910
3X-RAY DIFFRACTION3C915 - 920
4X-RAY DIFFRACTION4A1001 - 1064

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