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- PDB-5lz6: 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: 5lz6 | ||||||
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Title | Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus B | ||||||
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![]() | ANTIVIRAL PROTEIN / ACBD3 / GOLD / 3A / Aichivirus | ||||||
Function / homology | ![]() fatty-acyl-CoA binding / RNA-protein covalent cross-linking / : / : / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane ...fatty-acyl-CoA binding / RNA-protein covalent cross-linking / : / : / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / membrane => GO:0016020 / RNA helicase activity / symbiont entry into host cell / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / Golgi apparatus / mitochondrion / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klima, M. / Boura, E. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lz1SC ![]() 5lz3C 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: 19261.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4182.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Sugar | ChemComp-BGC / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.25 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97981 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.177 Å
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Refine LS restraints |
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LS refinement shell |
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