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- PDB-8eqb: FAM46C/BCCIPalpha/Nanobody complex -

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Basic information

Entry
Database: PDB / ID: 8eqb
TitleFAM46C/BCCIPalpha/Nanobody complex
Components
  • Isoform 2 of BRCA2 and CDKN1A-interacting protein
  • Synthetic nanobody 1
  • Terminal nucleotidyltransferase 5C
KeywordsNUCLEAR PROTEIN / FAM46 / BCCIP / poly-A polymerase / alternative splicing
Function / homology
Function and homology information


polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA stabilization / negative regulation of cell differentiation / in utero embryonic development / centrosome / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Terminal nucleotidyltransferase / Nucleotidyltransferase / Domain of unknown function (DUF1693)
Similarity search - Domain/homology
Terminal nucleotidyltransferase 5C / Isoform 2 of BRCA2 and CDKN1A-interacting protein
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsLiu, S. / Chen, H. / Yin, Y. / Bai, X. / Zhang, X.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA220283 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143158 United States
Welch FoundationI-1702 United States
Welch FoundationI-1944 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 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 15, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 15, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 15, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 15, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 15, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 15, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 15, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 15, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
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Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.3May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synthetic nanobody 1
B: Terminal nucleotidyltransferase 5C
C: Isoform 2 of BRCA2 and CDKN1A-interacting protein
D: Synthetic nanobody 1
E: Terminal nucleotidyltransferase 5C
F: Isoform 2 of BRCA2 and CDKN1A-interacting protein
G: Synthetic nanobody 1
H: Terminal nucleotidyltransferase 5C
I: Isoform 2 of BRCA2 and CDKN1A-interacting protein
J: Synthetic nanobody 1
K: Terminal nucleotidyltransferase 5C
L: Isoform 2 of BRCA2 and CDKN1A-interacting protein


Theoretical massNumber of molelcules
Total (without water)265,77112
Polymers265,77112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody
Synthetic nanobody 1


Mass: 13719.396 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein
Terminal nucleotidyltransferase 5C / Non-canonical poly(A) polymerase FAM46C


Mass: 24533.254 Da / Num. of mol.: 4 / Mutation: E166Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TENT5C, FAM46C / Production host: Escherichia coli (E. coli)
References: UniProt: Q5VWP2, polynucleotide adenylyltransferase
#3: Protein
Isoform 2 of BRCA2 and CDKN1A-interacting protein / P21- and CDK-associated protein 1 / Protein TOK-1


Mass: 28190.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCCIP, TOK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P287-2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: the complex between FAM46C and BCCIPalpha / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7376 / Symmetry type: POINT

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