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- PDB-7xt3: Crystal Structure of Hepatitis virus A 2C protein 128-335 aa -

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Basic information

Entry
Database: PDB / ID: 7xt3
TitleCrystal Structure of Hepatitis virus A 2C protein 128-335 aa
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / nonstructural Protein 2C
Function / homology
Function and homology information


host cell mitochondrial outer membrane / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / host multivesicular body / : ...host cell mitochondrial outer membrane / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / host multivesicular body / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 ...Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesHepatovirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, P. / Wojdyla, J.A. / Li, Z. / Wang, M. / Cui, S.
Funding support1items
OrganizationGrant numberCountry
Other privateCRP/CHN19-02
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Biochemical and structural characterization of hepatitis A virus 2C reveals an unusual ribonuclease activity on single-stranded RNA.
Authors: Chen, P. / Wojdyla, J.A. / Colasanti, O. / Li, Z. / Qin, B. / Wang, M. / Lohmann, V. / Cui, S.
History
DepositionMay 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7994
Polymers23,5141
Non-polymers2853
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-18 kcal/mol
Surface area10310 Å2
Unit cell
Length a, b, c (Å)50.165, 54.687, 85.666
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: 23513.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Depositor reference: GB NP_740555.1 / Source: (gene. exp.) Hepatovirus A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G4W9T5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.13 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. Cubic crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.45 mM Ammonium phosphate monobasic / PH range: 4.1-4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→43.29 Å / Num. obs: 24694 / % possible obs: 99.9 % / Redundancy: 4.305 % / Biso Wilson estimate: 46.223 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.172 / Χ2: 1.115 / Net I/σ(I): 7.67 / Num. measured all: 106315
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.284.3981.7890.8117636402840100.3212.03799.6
2.28-2.444.3531.0981.3616133370837060.5191.25399.9
2.44-2.644.1050.717214493353135310.6740.826100
2.64-2.894.3340.433.4213822319231890.8630.49199.9
2.89-3.234.220.2346.1512259290729050.950.26899.9
3.23-3.724.470.11811.8611421255625550.9890.134100
3.72-4.554.2680.06220.839305218021800.9960.071100
4.55-6.44.1770.05322.716976167116700.9970.06199.9
6.4-43.294.5040.03533.3542709559480.9990.0499.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.29 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 29.5 / Stereochemistry target values: ML / Details: Native-SAD
RfactorNum. reflection% reflection
Rfree0.2576 1221 4.95 %
Rwork0.2228 23426 -
obs0.2245 24647 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.42 Å2 / Biso mean: 59.6154 Å2 / Biso min: 19.89 Å2
Refinement stepCycle: final / Resolution: 2.15→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 15 40 1420
Biso mean--67.24 50.35 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.240.45471390.35952615275499
2.24-2.340.32391370.322625762713100
2.34-2.460.3251350.286626242759100
2.46-2.620.27941380.271125942732100
2.62-2.820.27091340.248125982732100
2.82-3.10.25681370.214125962733100
3.11-3.550.29291370.211426302767100
3.55-4.480.18641300.179725932723100
4.48-43.290.24491340.204526002734100

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