Crystal structure of FAM46B (TENT5B)

Experimental Data Snapshot

  • Resolution: 2.69 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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This is version 1.3 of the entry. See complete history


FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells.

Hu, J.L.Liang, H.Zhang, H.Yang, M.Z.Sun, W.Zhang, P.Luo, L.Feng, J.X.Bai, H.Liu, F.Zhang, T.Yang, J.Y.Gao, Q.Long, Y.Ma, X.Y.Chen, Y.Zhong, Q.Yu, B.Liao, S.Wang, Y.Zhao, Y.Zeng, M.S.Cao, N.Wang, J.Chen, W.Yang, H.T.Gao, S.

(2020) Nucleic Acids Res 48: 2733-2748

  • DOI: https://doi.org/10.1093/nar/gkaa049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Family with sequence similarity (FAM46) proteins are newly identified metazoan-specific poly(A) polymerases (PAPs). Although predicted as Gld-2-like eukaryotic non-canonical PAPs, the detailed architecture of FAM46 proteins is still unclear. Exact biological functions for most of FAM46 proteins also remain largely unknown. Here, we report the first crystal structure of a FAM46 protein, FAM46B. FAM46B is composed of a prominently larger N-terminal catalytic domain as compared to known eukaryotic PAPs, and a C-terminal helical domain. FAM46B resembles prokaryotic PAP/CCA-adding enzymes in overall folding as well as certain inter-domain connections, which distinguishes FAM46B from other eukaryotic non-canonical PAPs. Biochemical analysis reveals that FAM46B is an active PAP, and prefers adenosine-rich substrate RNAs. FAM46B is uniquely and highly expressed in human pre-implantation embryos and pluripotent stem cells, but sharply down-regulated following differentiation. FAM46B is localized to both cell nucleus and cytosol, and is indispensable for the viability of human embryonic stem cells. Knock-out of FAM46B is lethal. Knock-down of FAM46B induces apoptosis and restricts protein synthesis. The identification of the bacterial-like FAM46B, as a pluripotent stem cell-specific PAP involved in the maintenance of translational efficiency, provides important clues for further functional studies of this PAP in the early embryonic development of high eukaryotes.

  • Organizational Affiliation

    State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terminal nucleotidyltransferase 5B
A, B, C
402Xenopus tropicalisMutation(s): 0 
Gene Names: tent5bfam46b
Find proteins for F7E7M3 (Xenopus tropicalis)
Explore F7E7M3 
Go to UniProtKB:  F7E7M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7E7M3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.69 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.605α = 90
b = 76.12β = 96.51
c = 135.075γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Refinement description