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- PDB-8exe: Crystal structure of human FAM46A-BCCIPa complex at 3.5 angstrom ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8exe | ||||||
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Title | Crystal structure of human FAM46A-BCCIPa complex at 3.5 angstrom resolution | ||||||
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![]() | TRANSFERASE / Poly(A) polymerases / Inhibition | ||||||
Function / homology | ![]() polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA stabilization / regulation of ossification / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to bacterium / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, S. / Zhang, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. Authors: Shun Liu / Hua Chen / Yan Yin / Defen Lu / Guoming Gao / Jie Li / Xiao-Chen Bai / Xuewu Zhang / ![]() Abstract: The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report ...The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.8 KB | Display | ![]() |
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PDB format | ![]() | 163.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
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Full document | ![]() | 443 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eqbC ![]() 8exfC ![]() 6w36S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 38395.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96IP4, polynucleotide adenylyltransferase |
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#2: Protein | Mass: 30973.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris pH 7.5, 0.4 % v/v Jeffamine ED-2001, and 0.5-0.6 M Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 10371 / % possible obs: 96.3 % / Redundancy: 4.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.088 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.5→3.56 Å / Rmerge(I) obs: 1.277 / Num. unique obs: 478 / CC1/2: 0.521 / Rpim(I) all: 0.67 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6W36 Resolution: 3.5→44.46 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→44.46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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