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- PDB-5f8l: Enterovirus 71 Polymerase Elongation Complex (C3S1 Form) -

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Basic information

Entry
Database: PDB / ID: 5f8l
TitleEnterovirus 71 Polymerase Elongation Complex (C3S1 Form)
Components
  • Genome polyprotein
  • RNA (35-MER)
  • RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3')
KeywordsTRANSFERASE/RNA / polymerase-RNA complex / elongation / nucleotide addition cycle / TRANSFERASE-RNA complex
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 / channel activity / monoatomic ion transmembrane transport ...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 / 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 / RNA-directed RNA polymerase / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.812 Å
AuthorsShu, B. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology2013CB9111 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation
Authors: Shu, B. / Gong, P.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: RNA (35-MER)
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5184
Polymers70,4533
Non-polymers651
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-65 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.228, 76.709, 151.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Genome polyprotein


Mass: 53380.406 Da / Num. of mol.: 1 / Fragment: UNP residues 1732-2193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: E5RPG2, RNA-directed RNA polymerase
#2: RNA chain RNA (35-MER)


Mass: 11260.732 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*GP*AP*GP*AP*GP*AP*CP*C)-3')


Mass: 5811.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.085M MES pH 6.5, 25.5 %(w/v) PEG 5000 monomethyl ether, 15%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.81→60 Å / Num. obs: 18195 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 50.26 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.044 / Rrim(I) all: 0.111 / Χ2: 1.049 / Net I/av σ(I): 18.59 / Net I/σ(I): 8.2 / Num. measured all: 116789
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.81-2.916.60.517870.9210.2110.5431.033100
2.91-3.036.60.37417570.9530.1570.4061.093100
3.03-3.166.60.27918040.9770.1170.3031.084100
3.16-3.336.60.19217830.9850.0810.2091.09100
3.33-3.546.60.13817960.9920.0580.151.092100
3.54-3.816.50.1118140.9940.0470.121.054100
3.81-4.26.40.09318020.9950.040.1011.05199.9
4.2-4.86.30.08318350.9950.0360.0910.975100
4.8-6.056.10.07118500.9950.0310.0781.012100
6.05-606.10.04519670.9970.020.0491.00599.6

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OL6

3ol6


Resolution: 2.812→46.034 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 921 5.08 %
Rwork0.2003 17218 -
obs0.2022 18139 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.81 Å2 / Biso mean: 52.8227 Å2 / Biso min: 24.3 Å2
Refinement stepCycle: final / Resolution: 2.812→46.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 468 1 96 4242
Biso mean--46.94 45.22 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094292
X-RAY DIFFRACTIONf_angle_d1.1635927
X-RAY DIFFRACTIONf_chiral_restr0.047667
X-RAY DIFFRACTIONf_plane_restr0.007683
X-RAY DIFFRACTIONf_dihedral_angle_d14.9531639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8116-2.95990.31831290.22912329245896
2.9599-3.14530.30731300.242624132543100
3.1453-3.3880.27211320.220924422574100
3.388-3.72890.25091250.198524432568100
3.7289-4.26810.2111330.175524762609100
4.2681-5.3760.2021280.178824932621100
5.376-46.03970.22411440.20826222766100

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