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- PDB-6hm8: Crystal structure of human ACBD3 GOLD domain in complex with 3A p... -

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Basic information

Entry
Database: PDB / ID: 6hm8
TitleCrystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein)
Components
  • Genome polyprotein
  • Golgi resident protein GCP60
KeywordsVIRAL PROTEIN / complex / Golgi / enterovirus / picornavirus
Function / homology
Function and homology information


fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / ribonucleoside triphosphate phosphatase 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 ...fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / ribonucleoside triphosphate phosphatase 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 / 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 / Golgi membrane / symbiont-mediated activation of host autophagy / 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 / Golgi apparatus / mitochondrion / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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. / 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
Genome polyprotein / Golgi resident protein GCP60
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.277 Å
AuthorsKlima, M. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation17-07058Y Czech Republic
CitationJournal: Plos Pathog. / Year: 2019
Title: Convergent evolution in the mechanisms of ACBD3 recruitment to picornavirus replication sites.
Authors: Horova, V. / Lyoo, H. / Rozycki, B. / Chalupska, D. / Smola, M. / Humpolickova, J. / Strating, J.R.P.M. / van Kuppeveld, F.J.M. / Boura, E. / Klima, M.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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: Golgi resident protein GCP60
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)24,9002
Polymers24,9002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-11 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.361, 55.659, 64.372
Angle α, β, γ (deg.)90.00, 111.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Golgi resident protein GCP60 / Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi ...Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi phosphoprotein 1 / GOLPH1 / PBR- and PKA-associated protein 7 / Peripheral benzodiazepine receptor-associated protein PAP7


Mass: 19389.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD3, GCP60, GOCAP1, GOLPH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H3P7
#2: Protein/peptide Genome polyprotein


Mass: 5511.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2K9Y515, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 6% v/v 1,5-pentanediol, 14% v/v PEG 200, 10 mM spermine, 10 mM spermidine, 10 mM DL-ornithine, 10 mM 1,4-diaminobutane, 200 mM NaCl, 100 mM GlyGly/AMPD pH 8.5

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Data collection

DiffractionMean temperature: 100 K
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: 2.277→41.22 Å / Num. obs: 14316 / % possible obs: 97.75 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05062 / Rrim(I) all: 0.05929 / Net I/σ(I): 13.99
Reflection shellResolution: 2.277→2.359 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4869 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1310 / CC1/2: 0.881 / % possible all: 90.41

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDS11-Sep-2018data reduction
XDS11-Sep-2018data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LZ1

5lz1


Resolution: 2.277→41.22 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 715 5 %random selection
Rwork0.2177 ---
obs0.2186 14304 97.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.8 Å2
Refinement stepCycle: LAST / Resolution: 2.277→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 0 0 1401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061441
X-RAY DIFFRACTIONf_angle_d0.9541963
X-RAY DIFFRACTIONf_dihedral_angle_d13.101519
X-RAY DIFFRACTIONf_chiral_restr0.035209
X-RAY DIFFRACTIONf_plane_restr0.004251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2773-2.45310.32831370.29222600X-RAY DIFFRACTION94
2.4531-2.69990.30671440.26572733X-RAY DIFFRACTION99
2.6999-3.09040.29341430.2892723X-RAY DIFFRACTION98
3.0904-3.89320.27451450.23372744X-RAY DIFFRACTION99
3.8932-41.22670.16921460.17292789X-RAY DIFFRACTION98

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