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- PDB-6hm8: Crystal structure of human ACBD3 GOLD domain in complex with 3A p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hm8 | ||||||
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Title | Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein) | ||||||
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![]() | VIRAL PROTEIN / complex / Golgi / enterovirus / picornavirus | ||||||
Function / homology | ![]() : / fatty-acyl-CoA binding / RNA-protein covalent cross-linking / : / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity ...: / fatty-acyl-CoA binding / RNA-protein covalent cross-linking / : / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / 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 gene expression / RNA helicase activity / induction by virus of host autophagy / 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 / mitochondrion / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klima, M. / Boura, E. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 33.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.2 KB | Display | ![]() |
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Full document | ![]() | 421.9 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hlnC ![]() 6hltC ![]() 6hlvC ![]() 6hlwC ![]() 6hmvC ![]() 5lz1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19389.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 5511.147 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A2K9Y515, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
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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, 200 mM NaCl, 100 mM GlyGly/AMPD pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 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: 2.277→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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.277→41.22 Å
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Refine LS restraints |
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LS refinement shell |
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