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- PDB-6q69: Crystal structure of porcine ACBD3 GOLD domain in complex with 3A... -

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Basic information

Entry
Database: PDB / ID: 6q69
TitleCrystal structure of porcine ACBD3 GOLD domain in complex with 3A protein of enterovirus-G1
Components
  • Genome polyprotein
  • Peripherial benzodiazepine receptor associated protein
KeywordsVIRAL PROTEIN / complex / enterovirus / picornavirus
Function / homology
Function and homology information


: / : / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane ...: / : / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / symbiont-mediated suppression of host gene expression / DNA replication / 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 / membrane / nucleus / metal ion binding
Similarity search - Function
Golgi-dynamics membrane-trafficking / GOLD domain superfamily / GOLD domain / GOLD domain profile. / 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 ...Golgi-dynamics membrane-trafficking / GOLD domain superfamily / GOLD domain / GOLD domain profile. / 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 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. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Peripherial benzodiazepine receptor associated protein / Genome polyprotein
Similarity search - Component
Biological speciesSus scrofa (pig)
Porcine enterovirus 9
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.747 Å
AuthorsSmola, M. / Boura, E. / Klima, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation17-07058Y Czech Republic
CitationJournal: Arch. Virol. / Year: 2020
Title: Structural basis for hijacking of the host ACBD3 protein by bovine and porcine enteroviruses and kobuviruses.
Authors: Smola, M. / Horova, V. / Boura, E. / Klima, M.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Peripherial benzodiazepine receptor associated protein
B: Genome polyprotein
C: Peripherial benzodiazepine receptor associated protein
D: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)51,8484
Polymers51,8484
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-32 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.846, 55.767, 61.163
Angle α, β, γ (deg.)96.18, 105.54, 112.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peripherial benzodiazepine receptor associated protein


Mass: 19486.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DUB6
#2: Protein Genome polyprotein / 3A


Mass: 6437.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine enterovirus 9 / Strain: UKG/410/73 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8QUZ8, UniProt: O41174*PLUS

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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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12,5% w/v PEG 4000, 20% v/v 1,2,6-hexanetriol, 30mM lithium sulfate, 30mM sodium sulfate, 30mM pottasium sulfate, 100mM GlyGly/AMPD pH 8,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.747→30.16 Å / Num. obs: 14434 / % possible obs: 88.55 % / Redundancy: 2.1 % / Biso Wilson estimate: 56.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08092 / Rrim(I) all: 0.1092 / Net I/σ(I): 8.37
Reflection shellResolution: 2.747→2.846 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.6024 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 1306 / CC1/2: 0.72 / % possible all: 80.62

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LZ1

5lz1


Resolution: 2.747→30.156 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 721 5.02 %random selection
Rwork0.2284 ---
obs0.2305 14368 88.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.8 Å2
Refinement stepCycle: LAST / Resolution: 2.747→30.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 0 2784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032864
X-RAY DIFFRACTIONf_angle_d0.8083906
X-RAY DIFFRACTIONf_dihedral_angle_d11.3851032
X-RAY DIFFRACTIONf_chiral_restr0.031421
X-RAY DIFFRACTIONf_plane_restr0.003495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7475-2.95940.39511380.34882611X-RAY DIFFRACTION84
2.9594-3.25690.35541530.31162897X-RAY DIFFRACTION93
3.2569-3.72750.35651490.25322816X-RAY DIFFRACTION91
3.7275-4.69340.2211420.20362686X-RAY DIFFRACTION87
4.6934-30.15780.19871390.17412637X-RAY DIFFRACTION85

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