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- PDB-4nyz: The EMCV 3Dpol structure with altered motif A conformation at 2.1... -

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Basic information

Entry
Database: PDB / ID: 4nyz
TitleThe EMCV 3Dpol structure with altered motif A conformation at 2.15A resolution
ComponentsGenome polyprotein
KeywordsTRANSFERASE / Encephalomyocarditis virus / Close right hand / RNa dependent RNA polymerase
Function / homology
Function and homology information


positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity ...positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / 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 ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / 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 / 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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / Genome polyprotein
Similarity search - Component
Biological speciesMengo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVives-adrian, L. / Lujan, C. / Ferrer-orta, C. / Verdaguer, N.
CitationJournal: J.Virol. / Year: 2014
Title: The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site
Authors: Vives-Adrian, L. / Lujan, C. / Oliva, B. / van der Linden, L. / Selisko, B. / Coutard, B. / Canard, B. / van Kuppeveld, F.J. / Ferrer-Orta, C. / Verdaguer, N.
History
DepositionDec 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4754
Polymers52,2121
Non-polymers2633
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.553, 122.553, 198.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

21A-658-

HOH

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Components

#1: Protein Genome polyprotein / Leader protein / Protein VP0 / VP4-VP2 / Protein VP4 / P1A / Rho / Virion protein 4 / Protein VP2 / ...Leader protein / Protein VP0 / VP4-VP2 / Protein VP4 / P1A / Rho / Virion protein 4 / Protein VP2 / Beta / P1B / Virion protein 2 / Protein VP3 / Gamma / P1C / Virion protein 3 / Protein VP1 / Alpha / P1D / Virion protein 1 / Protein 2A / P2A / G / Protein 2B / I / P2B / Protein 2C / C / P2C / Protein 3A / P3A / Protein 3B / P3B / H / VPg / Protease 3C / P3C / Picornain 3C / p22 / RNA-directed RNA polymerase 3D-POL / E / P3D-POL


Mass: 52212.441 Da / Num. of mol.: 1 / Fragment: UNP residues 1834-2293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLyS
References: UniProt: P12296, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 110 / 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: 3.57 Å3/Da / Density % sol: 65.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10%PEG6000 and 2.0M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2013
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→104.3 Å / Num. all: 54658 / Num. obs: 40499 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.11 / Rsym value: 0.099 / Net I/σ(I): 6.4
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 18.7 / Rsym value: 0.77 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U09(THE HOMOLOGY MODEL HAS BEEN USED.)

1u09


Resolution: 2.15→104.3 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.575 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 2036 5 %RANDOM
Rwork0.22948 ---
all0.23061 54658 --
obs0.23061 38457 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.315 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å2-0 Å20 Å2
2--0.96 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.15→104.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 17 110 3807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193806
X-RAY DIFFRACTIONr_bond_other_d0.0010.023623
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.9715158
X-RAY DIFFRACTIONr_angle_other_deg0.738337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7275463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17223.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2415646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7871531
X-RAY DIFFRACTIONr_chiral_restr0.0520.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02891
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_it0.5282.4781852
X-RAY DIFFRACTIONr_mcbond_other0.5282.4771851
X-RAY DIFFRACTIONr_mcangle_it0.9763.7132315
X-RAY DIFFRACTIONr_mcangle_other0.9763.7142316
X-RAY DIFFRACTIONr_scbond_it0.4132.4941953
X-RAY DIFFRACTIONr_scbond_other0.4142.4941953
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.753.7212844
X-RAY DIFFRACTIONr_long_range_B_refined2.87119.5154274
X-RAY DIFFRACTIONr_long_range_B_other2.87119.5194275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 146 -
Rwork0.307 2816 -
obs--98.31 %
Refinement TLS params.Method: refined / Origin x: -7.6644 Å / Origin y: -29.2899 Å / Origin z: -23.9081 Å
111213212223313233
T0.0629 Å2-0.0018 Å20.0182 Å2-0.0695 Å20.0033 Å2--0.035 Å2
L0.6692 °2-0.2524 °20.3984 °2-1.3987 °2-0.0213 °2--2.0261 °2
S-0.0219 Å °0.0185 Å °0.1301 Å °-0.1688 Å °-0.0111 Å °-0.0899 Å °-0.0865 Å °0.3273 Å °0.033 Å °

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