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- PDB-6q68: Crystal structure of bovine ACBD3 GOLD domain in complex with 3A ... -

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Basic information

Entry
Database: PDB / ID: 6q68
TitleCrystal structure of bovine ACBD3 GOLD domain in complex with 3A protein of enterovirus-F2 (fusion protein)
Components
  • Acyl-CoA binding domain containing 3
  • Genome polyprotein
KeywordsVIRAL PROTEIN / complex / enterovirus / picornavirus
Function / homology
Function and homology information


Golgi Associated Vesicle Biogenesis / fatty-acyl-CoA binding / : / protein kinase A regulatory subunit binding / cytoplasmic vesicle membrane / 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 ...Golgi Associated Vesicle Biogenesis / fatty-acyl-CoA binding / : / protein kinase A regulatory subunit binding / cytoplasmic vesicle membrane / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / Golgi membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
: / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein ...: / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / FERM/acyl-CoA-binding protein superfamily / Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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
beta-D-glucopyranose / Acyl-CoA binding domain containing 3 / Genome polyprotein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Enterovirus F
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.161 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

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA binding domain containing 3
B: Genome polyprotein
C: Acyl-CoA binding domain containing 3
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8736
Polymers49,5134
Non-polymers3602
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-17 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.371, 55.371, 200.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Acyl-CoA binding domain containing 3


Mass: 19304.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ACBD3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F1MRE5
#2: Protein/peptide Genome polyprotein / 3A


Mass: 5452.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus F / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2LKY9, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#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.: 2
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: 3.11 Å3/Da / Density % sol: 60.44 %
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, 4% v/v 1,2-propandiol, 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: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.161→48.49 Å / Num. obs: 10318 / % possible obs: 99.78 % / Redundancy: 7.5 % / Biso Wilson estimate: 114.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07812 / Rrim(I) all: 0.08403 / Net I/σ(I): 16.06
Reflection shellResolution: 3.161→3.274 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 1049 / CC1/2: 0.662 / % possible all: 99.24

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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: 3.161→48.49 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.82
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 515 5 %random selection
Rwork0.2414 ---
obs0.243 10302 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 112.9 Å2
Refinement stepCycle: LAST / Resolution: 3.161→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 24 0 2728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032804
X-RAY DIFFRACTIONf_angle_d0.7743822
X-RAY DIFFRACTIONf_dihedral_angle_d13.628988
X-RAY DIFFRACTIONf_chiral_restr0.032414
X-RAY DIFFRACTIONf_plane_restr0.005482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1608-3.47880.30691290.30532449X-RAY DIFFRACTION100
3.4788-3.9820.28191290.27532456X-RAY DIFFRACTION100
3.982-5.0160.25331280.23272441X-RAY DIFFRACTION100
5.016-48.49520.27651290.22482441X-RAY DIFFRACTION99

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