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- PDB-4nz0: The EMCV 3Dpol structure at 2.8A resolution -

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Basic information

Entry
Database: PDB / ID: 4nz0
TitleThe EMCV 3Dpol structure at 2.8A 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 / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase ...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 / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / 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 ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / 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 / 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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMengo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVives-adrian, L. / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,23915
Polymers313,4676
Non-polymers7729
Water1,54986
1
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,2451
Polymers52,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,2451
Polymers52,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,2451
Polymers52,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5565
Polymers52,2451
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5214
Polymers52,2451
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4293
Polymers52,2451
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9858
Polymers104,4892
Non-polymers4966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)230.400, 140.786, 170.579
Angle α, β, γ (deg.)90.00, 125.86, 90.00
Int Tables number5
Space group name H-MC121

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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: 52244.504 Da / Num. of mol.: 6 / 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, RNA-directed RNA polymerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHOR STATES THE CONFLICT IS DUE TO THE USED CONSTRUCT.

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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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 4.0M Ammonium acetate, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979
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: 2.69→138.2 Å / Num. obs: 119540 / % possible obs: 98 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 16.3 / Rsym value: 0.49 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U09

1u09


Resolution: 2.8→138.2 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.917 / SU B: 49.959 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R: 0.92 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5370 5 %RANDOM
Rwork0.246 ---
obs0.247 101992 98.8 %-
all-275543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20.58 Å2
2---0.55 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.8→138.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22086 0 49 86 22221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01922690
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221619
X-RAY DIFFRACTIONr_angle_refined_deg0.7681.97230744
X-RAY DIFFRACTIONr_angle_other_deg0.669349750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.24652758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.33323.1951064
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.688153858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.44115188
X-RAY DIFFRACTIONr_chiral_restr0.0460.23384
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02125447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025297
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_it0.5814.92411041
X-RAY DIFFRACTIONr_mcbond_other0.5814.92411040
X-RAY DIFFRACTIONr_mcangle_it1.0897.38413793
X-RAY DIFFRACTIONr_mcangle_other1.0897.38413794
X-RAY DIFFRACTIONr_scbond_it0.284.92111647
X-RAY DIFFRACTIONr_scbond_other0.284.92111647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5897.37316951
X-RAY DIFFRACTIONr_long_range_B_refined2.14138.66425176
X-RAY DIFFRACTIONr_long_range_B_other2.14138.66525177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 398 -
Rwork0.379 7545 -
obs--98.84 %
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)
10.5990.2942-0.09971.14310.19451.862-0.0205-0.12070.07070.05360.04470.01830.1160.1872-0.02420.80570.0651-0.37460.2426-0.01570.183761.26991.833942.1227
21.48450.0407-0.0821.18740.37751.4136-0.213-0.0296-0.03970.30390.3198-0.3156-0.1333-0.0868-0.10680.98330.1175-0.43580.1331-0.09310.250454.723849.765534.528
30.64680.11010.19481.25510.10921.7370.07240.1381-0.0443-0.1882-0.2488-0.0132-0.0313-0.15550.17640.97090.1249-0.42850.2166-0.04710.21410.219175.559526.6779
41.63710.2437-0.1380.89160.25661.7168-0.11550.2348-0.1143-0.12070.03860.19680.08660.13450.07690.8190.0089-0.45960.098-0.02010.30823.2971-16.710137.651
50.51970.22820.5171.0066-0.11151.08690.0857-0.11320.001-0.07160.06170.07070.2538-0.0391-0.14740.9615-0.0629-0.44450.14090.02280.222642.095723.867-12.4811
60.78640.31670.45511.11330.29520.8858-0.0261-0.04110.0386-0.1067-0.0089-0.0062-0.11320.03160.0350.86760.0576-0.39770.1048-0.02740.19311.843224.97855.0105
70.07260.05830.00340.04970.00110.0022-0.03990.0078-0.0501-0.02920.0372-0.0237-0.0144-0.02780.00270.86230.0936-0.25490.41090.03260.328336.440215.941827.2968
80.2980.0586-0.58970.0155-0.12071.5541-0.0463-0.08030.08520.0571-0.0574-0.0159-0.15370.05520.10371.0241-0.0831-0.43140.10120.0390.67418.61712.53827.396
900000000000000-00.7043-0.2004-0.5010.2888-0.09290.6815.5114-4.29262.183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 460
2X-RAY DIFFRACTION2B1 - 460
3X-RAY DIFFRACTION3C1 - 460
4X-RAY DIFFRACTION4D1 - 460
5X-RAY DIFFRACTION5E1 - 460
6X-RAY DIFFRACTION6F1 - 460
7X-RAY DIFFRACTION7A501 - 529
8X-RAY DIFFRACTION7B501 - 506
9X-RAY DIFFRACTION7C501 - 504
10X-RAY DIFFRACTION7D601 - 607
11X-RAY DIFFRACTION7E601 - 625
12X-RAY DIFFRACTION7F601 - 614
13X-RAY DIFFRACTION8D501 - 503
14X-RAY DIFFRACTION8E501 - 503
15X-RAY DIFFRACTION8F501 - 502
16X-RAY DIFFRACTION9D504

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