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

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Basic information

Entry
Database: PDB / ID: 21tk
TitleEnterovirus 71 Polymerase (S417G mutant) Elongation Complex with Two Remdesivir Nucleotides Posing between Product Strand Positions -4/-5 and -6/-7, respectively (C3S6 form)
Components
  • Enterovirus 71 polymerase
  • RNA (34-MER)
  • RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*G*(F86)P*G*(F86)P*GP*CP*CP*U)-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: 1.9 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*(F86)P*G*(F86)P*GP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4276
Polymers70,1703
Non-polymers2583
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-89 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.234, 76.793, 154.908
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: C291M, S417G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / 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*(F86)P*G*(F86)P*GP*CP*CP*U)-3')


Mass: 5836.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 434 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
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: 1.9→50 Å / Num. obs: 57002 / % possible obs: 96.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 28.26 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Χ2: 1.014 / Net I/σ(I): 12.9 / Num. measured all: 314516
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.90.63244630.7540.9270.3470.7260.98776.6
1.97-2.054.70.42354160.910.9760.2110.4751.02993.4
2.05-2.145.60.2956500.9630.9910.1320.321.03296.2
2.14-2.2560.20357350.9830.9960.0880.2221.02398.5
2.25-2.3960.1558870.9890.9970.0650.1641.01399.9
2.39-2.585.90.11258580.9930.9980.050.1231.01399.9
2.58-2.845.50.08259150.9950.9990.0380.0911.011100
2.84-3.255.80.05859130.9970.9990.0260.064199.9
3.25-4.095.90.04559910.9980.9990.020.051.011100
4.09-505.40.04261740.9980.9990.0190.0461.01798.7

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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: 1.9→19.17 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 2834 4.98 %
Rwork0.1926 --
obs0.1942 56918 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 493 11 431 4568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074278
X-RAY DIFFRACTIONf_angle_d0.8515914
X-RAY DIFFRACTIONf_dihedral_angle_d19.531780
X-RAY DIFFRACTIONf_chiral_restr0.05670
X-RAY DIFFRACTIONf_plane_restr0.006677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.2641960.26471920X-RAY DIFFRACTION69
1.93-1.970.24661290.23432226X-RAY DIFFRACTION81
1.97-2.010.25321260.2152550X-RAY DIFFRACTION91
2.01-2.050.27821490.2072599X-RAY DIFFRACTION96
2.05-2.090.23411380.20092691X-RAY DIFFRACTION96
2.09-2.140.24161360.19262686X-RAY DIFFRACTION96
2.14-2.190.24051600.19082727X-RAY DIFFRACTION99
2.19-2.250.2361130.18692739X-RAY DIFFRACTION98
2.25-2.320.21571270.18892799X-RAY DIFFRACTION100
2.32-2.40.21931640.18712791X-RAY DIFFRACTION100
2.4-2.480.21231650.19022766X-RAY DIFFRACTION100
2.48-2.580.22511300.19522790X-RAY DIFFRACTION100
2.58-2.70.21051390.20222812X-RAY DIFFRACTION100
2.7-2.840.23431360.22829X-RAY DIFFRACTION100
2.84-3.020.1871480.19592788X-RAY DIFFRACTION100
3.02-3.250.24221620.1972804X-RAY DIFFRACTION100
3.25-3.570.19661510.1862830X-RAY DIFFRACTION100
3.57-4.080.20731420.17752879X-RAY DIFFRACTION100
4.09-5.130.20451480.16862886X-RAY DIFFRACTION100
5.13-19.170.26571750.2142972X-RAY DIFFRACTION99

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