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- PDB-5y6z: Crystal structure of the coxsackievirus A16 polymerase elongation... -

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Basic information

Entry
Database: PDB / ID: 5y6z
TitleCrystal structure of the coxsackievirus A16 polymerase elongation complex
Components
  • Genome polyprotein
  • Product RNA (14-MER)
  • Template RNA (33-MER)
KeywordsTRANSFERASE/RNA / polymerase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / : / 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 ...RNA-protein covalent cross-linking / : / : / 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 gene expression / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / 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 / 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
PHOSPHATE ION / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBi, P. / Shu, B. / Gong, P.
CitationJournal: Virol Sin / Year: 2017
Title: Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics
Authors: Bi, P. / Shu, B. / Gong, P.
History
DepositionAug 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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: Template RNA (33-MER)
C: Product RNA (14-MER)
E: Genome polyprotein
F: Template RNA (33-MER)
G: Product RNA (14-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,44317
Polymers137,4866
Non-polymers95711
Water6,792377
1
A: Genome polyprotein
B: Template RNA (33-MER)
C: Product RNA (14-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3049
Polymers68,7433
Non-polymers5616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-57 kcal/mol
Surface area22530 Å2
MethodPISA
2
E: Genome polyprotein
F: Template RNA (33-MER)
G: Product RNA (14-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1398
Polymers68,7433
Non-polymers3965
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-53 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.724, 93.724, 167.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein Genome polyprotein


Mass: 53566.812 Da / Num. of mol.: 2 / Fragment: UNP residues 1732-2193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pCG1 / References: UniProt: L7WS61

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RNA chain , 2 types, 4 molecules BFCG

#2: RNA chain Template RNA (33-MER)


Mass: 10649.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain Product RNA (14-MER)


Mass: 4526.756 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 388 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.09 Å3/Da / Density % sol: 60.19 % / Mosaicity: 0.454 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→46.03 Å / Num. obs: 56671 / % possible obs: 99.5 % / Redundancy: 2.93 % / Biso Wilson estimate: 41.55 Å2 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.158 / Χ2: 1.14 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
2.5-2.592.950.3722.157050.4481.2699.9
2.59-2.692.950.2952.656560.3571.1499.8
2.69-2.822.940.2792.957130.3361.1699.8
2.82-2.962.950.2293.456690.2771.1499.6
2.96-3.152.950.1694.257130.2031.1199.7
3.15-3.392.930.135.256200.1561.0599.6
3.39-3.732.930.1265.756710.151.0499.3
3.73-4.272.930.1226.356830.1441.1499.2
4.27-5.382.880.1146.456180.1361.1199
5.38-46.032.880.0888.656230.1071.2798.6

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Processing

Software
NameVersionClassification
d*TREK9.9.9.4Ddata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
d*TREK9.9.9.4Ddata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OL6

3ol6


Resolution: 2.5→32.829 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.05
RfactorNum. reflection% reflection
Rfree0.2594 2766 4.9 %
Rwork0.2183 --
obs0.2202 56421 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.15 Å2 / Biso mean: 46.0884 Å2 / Biso min: 23.06 Å2
Refinement stepCycle: final / Resolution: 2.5→32.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7247 1204 57 377 8885
Biso mean--51.24 44.46 -
Num. residues----974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088825
X-RAY DIFFRACTIONf_angle_d0.98512249
X-RAY DIFFRACTIONf_chiral_restr0.051394
X-RAY DIFFRACTIONf_plane_restr0.0071353
X-RAY DIFFRACTIONf_dihedral_angle_d16.8435075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.54320.35561320.30962711284399
2.5432-2.58940.30361410.295727112852100
2.5894-2.63920.4121540.28362629278399
2.6392-2.6930.33661230.27492697282099
2.693-2.75160.34471840.271927062890100
2.7516-2.81550.3408770.266827322809100
2.8155-2.88590.31041370.260926912828100
2.8859-2.96390.27711350.26292694282999
2.9639-3.0510.2671580.24326662824100
3.051-3.14950.31811560.24332720287699
3.1495-3.26190.26631520.22982643279599
3.2619-3.39240.27461410.21662659280099
3.3924-3.54660.28691700.21632667283799
3.5466-3.73340.21621440.20542688283299
3.7334-3.96690.24421370.19132666280399
3.9669-4.27260.19241040.17662746285099
4.2726-4.70140.20681430.17532653279699
4.7014-5.37920.21271480.17792651279999
5.3792-6.76740.25471300.21712692282299
6.7674-32.83140.23281000.2232633273396

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