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- PDB-5lz3: Crystal structure of human ACBD3 GOLD domain in complex with 3A p... -

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Basic information

Entry
Database: PDB / ID: 5lz3
TitleCrystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus A
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 / host cell Golgi membrane / protein kinase A regulatory subunit binding / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization ...fatty-acyl-CoA binding / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / host cell Golgi membrane / protein kinase A regulatory subunit binding / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / Golgi membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / mitochondrion / proteolysis / RNA 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. / LRAT domain profile. / LRAT domain / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily ...Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / LRAT domain profile. / LRAT domain / 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 / 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
Genome polyprotein / Golgi resident protein GCP60
Similarity search - Component
Biological speciesHomo sapiens (human)
Aichi virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Golgi resident protein GCP60
B: 3A


Theoretical massNumber of molelcules
Total (without water)25,8742
Polymers25,8742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-12 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.100, 81.150, 117.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 3A


Mass: 6612.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aichi virus / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O91464

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM MOPS/HEPES pH 7.5, 12.5% w/v PEG 1.000, 12.5% w/v PEG 3.350, 12.5% v/v MPD, 20mM D-glucose/D-mannose/D-galactose/L-fucose/D-xylose/N-acetyl-D-glucosamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3→26.36 Å / Num. obs: 5185 / % possible obs: 95.26 % / Redundancy: 4.1 % / Biso Wilson estimate: 51.86 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.2025 / Rsym value: 0.2025 / Net I/σ(I): 7.9 / Num. measured all: 21415
Reflection shellResolution: 3→3.107 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6965 / Mean I/σ(I) obs: 1.68 / CC1/2: 0.691 / % possible all: 96.55

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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: 3→26.36 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 260 5.02 %random selection
Rwork0.2184 ---
obs0.2199 5182 95.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 0 1301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051340
X-RAY DIFFRACTIONf_angle_d0.7681822
X-RAY DIFFRACTIONf_dihedral_angle_d12.945485
X-RAY DIFFRACTIONf_chiral_restr0.037188
X-RAY DIFFRACTIONf_plane_restr0.003234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.77830.28441300.23662461X-RAY DIFFRACTION98
3.7783-26.36230.22831300.20752461X-RAY DIFFRACTION93

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