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- PDB-8exf: Crystal structure of human FAM46A-BCCIPa complex at 3.2 angstrom ... -

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Basic information

Entry
Database: PDB / ID: 8exf
TitleCrystal structure of human FAM46A-BCCIPa complex at 3.2 angstrom resolution
Components
  • BCCIPa
  • Terminal nucleotidyltransferase 5A
KeywordsTRANSFERASE / Poly(A) polymerases / Inhibition
Function / homology
Function and homology information


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
Terminal nucleotidyltransferase / Domain of unknown function (DUF1693) / Nucleotidyltransferase
Similarity search - Domain/homology
Terminal nucleotidyltransferase 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsLiu, S. / Zhang, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA220283 United States
CitationJournal: Sci Adv / Year: 2023
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
DepositionOct 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terminal nucleotidyltransferase 5A
B: BCCIPa


Theoretical massNumber of molelcules
Total (without water)62,5042
Polymers62,5042
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.621, 188.145, 93.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Terminal nucleotidyltransferase 5A / HBV X-transactivated gene 11 protein / HBV XAg-transactivated protein 11


Mass: 38395.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TENT5A, C6orf37, FAM46A, XTP11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96IP4, polynucleotide adenylyltransferase
#2: Protein BCCIPa


Mass: 24108.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH8.0, 0.2 M Sodium thiocyanate, 15-18% PEG 3350.
PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13367 / % possible obs: 98.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 47.67 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.04 / Net I/σ(I): 17.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 671 / CC1/2: 0.462 / Rpim(I) all: 0.579 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Coot0.9.8model building
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W36

6w36


Resolution: 3.22→47.04 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 564 5 %
Rwork0.2071 --
obs0.2092 11277 83.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 0 1 3963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.629
X-RAY DIFFRACTIONf_dihedral_angle_d18.4061515
X-RAY DIFFRACTIONf_chiral_restr0.043623
X-RAY DIFFRACTIONf_plane_restr0.004697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.540.3388760.2631451X-RAY DIFFRACTION46
3.54-4.050.27971490.22432828X-RAY DIFFRACTION90
4.05-5.10.20761670.18713164X-RAY DIFFRACTION99
5.1-47.040.24841720.19983270X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75470.0969-0.22643.52640.142.32130.2243-0.09190.24180.2520.1847-0.3074-0.06690.07970.03570.21360.00450.11990.1308-0.03790.07928.348613.57557.8215
23.21081.2672.64153.2420.26153.2466-0.09360.47860.1168-0.09150.2343-1.125-0.12170.5462-0.12680.3782-0.1425-0.07590.8075-0.21510.85831.058628.772622.8723
34.38331.0504-0.724.5013-0.71143.7001-0.11760.03030.2256-0.1530.0193-0.2376-0.30930.30840.06940.3789-0.14520.17210.18240.07640.373612.141443.20261.0286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 289 )
2X-RAY DIFFRACTION2chain 'A' and (resid 290 through 391 )
3X-RAY DIFFRACTION3chain 'B'

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