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- PDB-5lz6: Crystal structure of human ACBD3 GOLD domain in complex with 3A p... -

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Basic information

Entry
Database: PDB / ID: 5lz6
TitleCrystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus B
Components
  • 3A
  • Golgi resident protein GCP60
KeywordsANTIVIRAL PROTEIN / ACBD3 / GOLD / 3A / Aichivirus
Function / homology
Function and homology information


fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / cytoplasmic vesicle membrane / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity ...fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / cytoplasmic vesicle membrane / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / Golgi membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / Golgi apparatus / mitochondrion / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
GOLD domain / : / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / LRAT domain / GOLD domain / GOLD domain profile. / LRAT domain profile. ...GOLD domain / : / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / LRAT domain / GOLD domain / GOLD domain profile. / LRAT 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 / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Genome polyprotein / Golgi resident protein GCP60
Similarity search - Component
Biological speciesHomo sapiens (human)
Aichivirus B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKlima, M. / Boura, E.
CitationJournal: Structure / Year: 2017
Title: Kobuviral Non-structural 3A Proteins Act as Molecular Harnesses to Hijack the Host ACBD3 Protein.
Authors: Klima, M. / Chalupska, D. / Rozycki, B. / Humpolickova, J. / Rezabkova, L. / Silhan, J. / Baumlova, A. / Dubankova, A. / Boura, E.
History
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 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: Golgi resident protein GCP60
B: 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6243
Polymers23,4442
Non-polymers1801
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-14 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.630, 55.630, 144.270
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 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: 19261.217 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 (bacteria) / References: UniProt: Q9H3P7
#2: Protein/peptide 3A


Mass: 4182.599 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aichivirus B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8BES6
#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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM MOPSO/Bis-Tris pH 6.5, 15% w/v PEG 3.000, 1% w/v DDAO, 10% 1,4-butanediol, 10% w/v glucose, 20mM L-arginine/L-threonine/L-histidine/betaine, 10mM trans-4-hydroxy-L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 2.6→48.18 Å / Num. obs: 8472 / % possible obs: 99.96 % / Redundancy: 10.4 % / Biso Wilson estimate: 77.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07815 / Rsym value: 0.07815 / Net I/σ(I): 22.47
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.984 / Mean I/σ(I) obs: 1.24 / CC1/2: 0.454 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSversion Oct 15, 2015data reduction
XDSversion Oct 15, 2015data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LZ1

5lz1


Resolution: 2.6→48.177 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 424 5.01 %random selection
Rwork0.2149 ---
obs0.2171 8471 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 12 0 1279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031316
X-RAY DIFFRACTIONf_angle_d0.7081794
X-RAY DIFFRACTIONf_dihedral_angle_d11.98463
X-RAY DIFFRACTIONf_chiral_restr0.028197
X-RAY DIFFRACTIONf_plane_restr0.003225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.97620.33461370.32012605X-RAY DIFFRACTION100
2.9762-3.74950.2871400.2672654X-RAY DIFFRACTION100
3.7495-48.18520.23971470.18012788X-RAY DIFFRACTION100

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