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- PDB-6q67: Crystal structure of porcine ACBD3 GOLD domain in complex with 3A... -

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Basic information

Entry
Database: PDB / ID: 6q67
TitleCrystal structure of porcine ACBD3 GOLD domain in complex with 3A protein of Aichivirus C
Components
  • 3A
  • Peripherial benzodiazepine receptor associated protein
KeywordsVIRAL PROTEIN / complex / aichivirus / picornavirus
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication ...RNA-protein covalent cross-linking / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / 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 / proteolysis / RNA binding / ATP binding
Similarity search - Function
Golgi-dynamics membrane-trafficking / GOLD domain superfamily / GOLD domain / GOLD domain profile. / 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 ...Golgi-dynamics membrane-trafficking / GOLD domain superfamily / GOLD domain / GOLD domain profile. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
beta-D-glucopyranose / Genome polyprotein / Peripherial benzodiazepine receptor associated protein
Similarity search - Component
Biological speciesSus scrofa (pig)
Aichivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 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: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4263
Polymers23,2462
Non-polymers1801
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-13 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.390, 55.390, 169.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Peripherial benzodiazepine receptor associated protein


Mass: 19486.404 Da / Num. of mol.: 1
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/peptide 3A


Mass: 3759.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aichivirus C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8R1T8*PLUS
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% w/v PEG 3000, 10% v/v 1,4-butanediol, 1% w/v N,N-dimethyldodecylamine-N-oxide , 10% w/v glucose, 20mM L-arginine, 20mM L-threonine, 20mM L-histidine, 20mM betaine, 10mM trans-4-hydroxy-L- ...Details: 15% w/v PEG 3000, 10% v/v 1,4-butanediol, 1% w/v N,N-dimethyldodecylamine-N-oxide , 10% w/v glucose, 20mM L-arginine, 20mM L-threonine, 20mM L-histidine, 20mM betaine, 10mM trans-4-hydroxy-L-proline, 100mM BES/TEA pH 7.5

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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: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.249→47.97 Å / Num. obs: 14951 / % possible obs: 99.07 % / Redundancy: 5.8 % / Biso Wilson estimate: 68.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03611 / Rrim(I) all: 0.0399 / Net I/σ(I): 21.49
Reflection shellResolution: 2.249→2.328 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1448 / CC1/2: 0.799 / % possible all: 97.57

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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: 2.249→47.969 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.76
RfactorNum. reflection% reflectionSelection details
Rfree0.268 746 5.01 %random selection
Rwork0.2344 ---
obs0.2361 14902 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79 Å2
Refinement stepCycle: LAST / Resolution: 2.249→47.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 12 0 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081301
X-RAY DIFFRACTIONf_angle_d1.1441774
X-RAY DIFFRACTIONf_dihedral_angle_d14.417458
X-RAY DIFFRACTIONf_chiral_restr0.041192
X-RAY DIFFRACTIONf_plane_restr0.008224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2486-2.42220.45141450.38412745X-RAY DIFFRACTION98
2.4222-2.66590.33751480.32962781X-RAY DIFFRACTION98
2.6659-3.05160.31721450.30092774X-RAY DIFFRACTION99
3.0516-3.84440.32581490.27242844X-RAY DIFFRACTION99
3.8444-47.980.21991590.18973012X-RAY DIFFRACTION100

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