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- PDB-5f8i: Enterovirus 71 Polymerase Elongation Complex (C1S2/3 Form) -

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Basic information

Entry
Database: PDB / ID: 5f8i
TitleEnterovirus 71 Polymerase Elongation Complex (C1S2/3 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*A)-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
CYTIDINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsShu, B. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6289
Polymers69,8423
Non-polymers7856
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-95 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.669, 77.310, 149.656
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: 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

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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*A)-3')


Mass: 5201.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 150 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.085 M 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: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. obs: 26095 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 54.03 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.032 / Rrim(I) all: 0.068 / Χ2: 0.96 / Net I/av σ(I): 20.14 / Net I/σ(I): 12.1 / Num. measured all: 112185
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.594.30.48225410.8240.2630.551.005100
2.59-2.694.30.35425700.9080.1930.4051.038100
2.69-2.824.30.26425770.9480.1430.3011.056100
2.82-2.964.30.17625740.9720.0960.2011.0599.8
2.96-3.154.30.11925990.9890.0650.1361.00399.8
3.15-3.394.30.07625980.9960.0410.0860.99999.8
3.39-3.734.30.06326050.9960.0340.0720.90899.6
3.73-4.274.20.05626110.9960.0310.0640.7999.3
4.27-5.384.30.04826340.9960.0260.0550.81299.4
5.38-604.50.0327860.9990.0160.0340.94598.7

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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: 2.503→32.265 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1328 5.1 %
Rwork0.1994 24717 -
obs0.2017 26045 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.28 Å2 / Biso mean: 59.054 Å2 / Biso min: 35.08 Å2
Refinement stepCycle: final / Resolution: 2.503→32.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 471 43 144 4339
Biso mean--53.7 55.55 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084339
X-RAY DIFFRACTIONf_angle_d1.1985996
X-RAY DIFFRACTIONf_chiral_restr0.047671
X-RAY DIFFRACTIONf_plane_restr0.006684
X-RAY DIFFRACTIONf_dihedral_angle_d16.0831658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5031-2.60320.35371510.26562631278298
2.6032-2.72170.30891350.256627342869100
2.7217-2.86510.31211540.248127262880100
2.8651-3.04450.30671440.233827142858100
3.0445-3.27930.29281460.21727132859100
3.2793-3.60890.24091410.199827472888100
3.6089-4.13020.20551470.17762757290499
4.1302-5.20010.22771490.173927932942100
5.2001-32.26770.21581610.19212902306399

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