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Yorodumi- PDB-6hln: Crystal structure of human ACBD3 GOLD domain in complex with 3A p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hln | ||||||
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Title | Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 | ||||||
Components |
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Keywords | VIRAL PROTEIN / complex / Golgi / enterovirus / picornavirus | ||||||
Function / homology | Function and homology information fatty-acyl-CoA binding / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / protein sequestering activity ...fatty-acyl-CoA binding / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / protein sequestering activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / : / symbiont-mediated suppression of host toll-like receptor signaling pathway / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / Golgi membrane / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / mitochondrion / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) enterovirus D68 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Klima, M. / Boura, E. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hln.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hln.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/6hln ftp://data.pdbj.org/pub/pdb/validation_reports/hl/6hln | HTTPS FTP |
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-Related structure data
Related structure data | 6hltC 6hlvC 6hlwC 6hm8C 6hmvC 5lz1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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(DE3) (bacteria) / References: UniProt: Q9H3P7 |
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#2: Protein | Mass: 7035.023 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: Q68T42, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.16 % |
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Crystal grow | Temperature: 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, 300 mM NaCl, 100 mM GlyGly/AMPD pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.45 Å / Num. obs: 18521 / % possible obs: 98.34 % / Redundancy: 3.8 % / Biso Wilson estimate: 47.36 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.78 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.21 / Num. unique obs: 1848 / CC1/2: 0.556 / % possible all: 99.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LZ1 Resolution: 2.1→47.45 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.45 Å
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Refine LS restraints |
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LS refinement shell |
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