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- PDB-6lsf: Crystal structure of the enterovirus 71 polymerase elongation com... -

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Basic information

Entry
Database: PDB / ID: 6lsf
TitleCrystal structure of the enterovirus 71 polymerase elongation complex (C2S6RA/C2S6RB 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/DNA / polymerase-RNA complex / elongation / translocation intermediate / TRANSFERASE-DNA 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / 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) / 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 / 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 speciesHuman enterovirus 71
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.152 Å
AuthorsWang, M. / Shu, B. / Jing, X. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
CitationJournal: Nat Commun / Year: 2020
Title: Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures.
Authors: Wang, M. / Li, R. / Shu, B. / Jing, X. / Ye, H.Q. / Gong, P.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 10, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)70,6425
Polymers70,4813
Non-polymers1612
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-68 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.350, 76.447, 155.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Genome polyprotein


Mass: 53408.461 Da / Num. of mol.: 1 / Mutation: C291M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 (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)

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Non-polymers , 3 types, 94 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5 / Details: MES, PEG 5000 monomethyl ether, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 36176 / % possible obs: 89.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.034 / Rrim(I) all: 0.076 / Χ2: 0.989 / Net I/σ(I): 12.1 / Num. measured all: 170510
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.233.70.40826550.8780.220.4660.92966.8
2.23-2.324.10.3330510.9350.1710.3740.99276.6
2.32-2.424.80.26633660.9640.1280.2970.95784.9
2.42-2.555.20.22636680.9720.1050.250.99191.6
2.55-2.715.10.17238520.9820.0830.1921.03996.7
2.71-2.925.20.12839530.9880.0610.1421.05198.5
2.92-3.214.90.0939720.9930.0450.1011.01498.3
3.21-3.684.70.06639010.9950.0340.0750.98496.5
3.68-4.634.30.05337960.9940.0290.0610.94292.6
4.63-504.70.04939620.9950.0250.0550.93792.1

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F8L

5f8l


Resolution: 2.152→28.729 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 1847 5.12 %
Rwork0.2151 34256 -
obs0.2169 36103 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.33 Å2 / Biso mean: 54.1672 Å2 / Biso min: 31.8 Å2
Refinement stepCycle: final / Resolution: 2.152→28.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 405 6 92 4124
Biso mean--47.77 49.64 -
Num. residues----482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1522-2.21040.34651050.2687187564
2.2104-2.27540.3282900.2548216173
2.2754-2.34890.31541240.2485232781
2.3489-2.43280.28031300.2493249986
2.4328-2.53010.26231600.2487266192
2.5301-2.64520.30561740.2506276496
2.6452-2.78450.29851270.2552289398
2.7845-2.95880.32461620.2471287199
2.9588-3.1870.32651450.2552291098
3.187-3.50720.28871570.2253285897
3.5072-4.01360.23211620.1977279694
4.0136-5.05220.20511650.1732273592
5.0522-28.7290.20461460.2019290692

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