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- PDB-21th: Enterovirus 71 Polymerase (S417G mutant) Elongation Complex with ... -

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Basic information

Entry
Database: PDB / ID: 21th
TitleEnterovirus 71 Polymerase (S417G mutant) Elongation Complex with Remdesivir Nucleotides at Product Strand Positions -2 and -4 (C1S1 form)
Components
  • Enterovirus 71 polymerase
  • RNA (34-MER)
  • RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*G)-D(*R)-R(P*G)-D(*R)-R(P*G)-3')
KeywordsTRANSFERASE / enterovirus / RNA-dependent RNA polymerase / elongation complex / remdesivir nucleotide
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / virion attachment to host cell / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...: / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsLi, R. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Highly effective viral RdRP translocation hindrance by the remdesivir nucleotide
Authors: Li, R. / Shao, Q. / Wang, M. / Feng, C. / Xu, Q. / Wang, Q. / Shang, L.
History
DepositionDec 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterovirus 71 polymerase
B: RNA (34-MER)
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*G)-D(*R)-R(P*G)-D(*R)-R(P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7038
Polymers69,2533
Non-polymers4505
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-114 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.160, 77.177, 153.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Enterovirus 71 polymerase


Mass: 53378.434 Da / Num. of mol.: 1 / Mutation: S417G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pCG1
References: UniProt: E5RPG3, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (34-MER)


Mass: 10954.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*G)-D(*R)-R(P*G)-D(*R)-R(P*G)-3')


Mass: 4920.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 195 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.5
Details: 0.17 M ammonium sulfate, 0.2125 M MES (pH 6.5), 25.5% (wt./vol.) PEG5000 monomethyl ether, and 15% (vol./vol.) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 36262 / % possible obs: 97.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.85 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.05 / Rrim(I) all: 0.101 / Χ2: 1.027 / Net I/σ(I): 9.1 / Num. measured all: 143165
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.23-2.313.80.60833110.7780.9360.3330.6960.99690.2
2.31-2.440.51635370.850.9590.2820.5911.00996.8
2.4-2.514.10.42536610.8990.9730.2320.4861.03499.6
2.51-2.644.10.31336540.9310.9820.1730.3591.06299.4
2.64-2.813.80.20936420.9670.9920.120.2421.02899.7
2.81-3.0340.14636950.9830.9960.0820.1681.05299.8
3.03-3.334.20.09637170.9910.9980.0520.111.03799.7
3.33-3.814.10.07136910.9930.9980.040.0821.02299.1
3.81-4.83.70.05636350.9940.9980.0330.0661.01496.2
4.8-503.60.0537190.9960.9990.0290.0581.00593.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→24.4 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1804 4.99 %
Rwork0.2019 --
obs0.2037 36163 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 476 21 190 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084236
X-RAY DIFFRACTIONf_angle_d0.8985856
X-RAY DIFFRACTIONf_dihedral_angle_d18.688768
X-RAY DIFFRACTIONf_chiral_restr0.05660
X-RAY DIFFRACTIONf_plane_restr0.006671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.290.31291110.26562321X-RAY DIFFRACTION86
2.29-2.360.31121250.26272524X-RAY DIFFRACTION94
2.36-2.440.29831520.24552648X-RAY DIFFRACTION99
2.44-2.520.30991520.23292666X-RAY DIFFRACTION100
2.52-2.630.28351230.23332690X-RAY DIFFRACTION99
2.63-2.750.26431330.21732680X-RAY DIFFRACTION100
2.75-2.890.23141430.222683X-RAY DIFFRACTION100
2.89-3.070.23271410.22762704X-RAY DIFFRACTION100
3.07-3.310.2591520.21252694X-RAY DIFFRACTION100
3.31-3.640.23451430.20012696X-RAY DIFFRACTION99
3.64-4.160.22351300.17052710X-RAY DIFFRACTION98
4.16-5.240.18821340.17192662X-RAY DIFFRACTION95
5.24-24.40.22311650.19822681X-RAY DIFFRACTION93

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