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- PDB-5xe0: Crystal structure of EV-D68-3Dpol in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5xe0
TitleCrystal structure of EV-D68-3Dpol in complex with GTP
ComponentsGenome polyprotein
KeywordsHYDROLASE / thermostability / RNA-dependent RNA polymerase
Function / homology
Function and homology information


: / RNA-protein covalent cross-linking / : / : / 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 / : / : / 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 / symbiont-mediated suppression of host gene expression / 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
GUANOSINE-5'-TRIPHOSPHATE / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus D68
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXie, W. / Wang, C. / Wang, Z. / Li, Q. / Wang, C.
Funding support China, 2items
OrganizationGrant numberCountry
GuangDong Province2011Y038 China
16lgjc76 China
CitationJournal: J. Virol. / Year: 2017
Title: Crystal Structure and Thermostability Characterization of Enterovirus D68 3Dpol
Authors: Wang, C. / Wang, C. / Li, Q. / Wang, Z. / Xie, W.
History
DepositionMar 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6132
Polymers53,0901
Non-polymers5231
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-2 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.093, 81.436, 58.446
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Genome polyprotein


Mass: 53089.535 Da / Num. of mol.: 1 / Fragment: UNP residues 1732-2188 / Mutation: V17A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Production host: Escherichia coli (E. coli) / References: UniProt: F1T146
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 20.1% isopropanol, 20.1% PEG 3350
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→26.21 Å / Num. obs: 21405 / % possible obs: 98.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.201 / Net I/av σ(I): 6 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3156 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACccp4 6.5refinement
CrysalisProv.1.171.33.49data reduction
CrysalisProv.1.171.33.49data scaling
PHENIX1.10.1phasing
PHENIX(1.10.1_2155: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n6m

3n6m


Resolution: 2.3→26.21 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.56
RfactorNum. reflection% reflection
Rfree0.2667 1092 5.11 %
Rwork0.2236 --
obs0.2258 21378 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 32 243 3882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033740
X-RAY DIFFRACTIONf_angle_d0.5645077
X-RAY DIFFRACTIONf_dihedral_angle_d13.3452230
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40480.34051320.30462574X-RAY DIFFRACTION100
2.4048-2.53140.36731310.30342577X-RAY DIFFRACTION100
2.5314-2.68990.3651240.28622560X-RAY DIFFRACTION99
2.6899-2.89730.34391280.2832584X-RAY DIFFRACTION99
2.8973-3.18850.30771610.25092515X-RAY DIFFRACTION99
3.1885-3.64880.23681220.21262541X-RAY DIFFRACTION98
3.6488-4.5930.20781540.16552496X-RAY DIFFRACTION97
4.593-26.21470.2151400.17352439X-RAY DIFFRACTION93

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