Entry created on 1 July 2019 (Revision 1.0) Annotator: Rita Pancsa; Orsolya Kovács
Basic protein information
Accession Q14103
Common name HNRNPD
Gene HNRNPD
Organism Homo sapiens
Uniprot name Heterogeneous nuclear ribonucleoprotein D0
Basic LLPS information
Organelle nuclear body; ribonucleoprotein complex; Sam68 nuclear bodies (SNBs)
Type of experimental evidence
Protein region(s) mediating LLPS
1
-
355
Full protein sequence contributes to LLPS: RRMs and G/Q/Y-rich PLD
Based on the experimental results of the following publication: 27377249
Molecular features viewer
PDB structures
Extended LLPS information
Functional description
Sam68 and HNRNPD are essential for the formation of the RNase-sensitive Sam68 nuclear bodies (SNBs). Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures. Both the two RRMs (and their intact RNA-binding capability) and the PLD of HNRNPD are required for SNB localization and assembly. The functional PLD is required primarily for Sam68 interaction and for the homodimeric interaction of HNRNPD in SNBs. In vitro LLPS experiments with these constructs are lacking (PMID:27377249).
Literature supporting the LLPS: 27377249, 28709000
Functional class of membraneless organelle: not known/not clear
Binding partners (at biological protein concentrations)
1) RNA (not only for SNB localization but also for SNB formation)
Type of RNA(s) required/used for the LLPS at biological protein concentrations
cellular RNA
Molecular interaction types contributing to LLPS
protein-RNA interaction (PMID:27377249) cation-π (cation-pi) interactions (PMID:28709000) π-π (pi-pi) interactions (PMID:28709000)
Determinants of phase separation and droplet properties
N/A
Membrane cluster No
Partner-dependent Yes
RNA-dependent Yes
PTM required Not known
Domain-motif interactions No
Discrete oligomerization Yes
Regulation and disease
Post-translational modifications affecting LLPS
Position Residue PTM Effect Reference Modifying enzyme Notes
Isoforms known to affect LLPS
Isoform Effect Reference
All known isoforms containing sequence changes in the LLPS region(s)
Position type Isoform names from UniProt
Disease mutations affecting LLPS
Mutation dbSNP Disease OMIM Effect Reference Notes
Experimental information
Experimental techniques applied to prove/investigate LLPS
In vivo, SNBs disappeared upon a temperature shift from 37 to 32°C for 24 h and reformed when the temperature was returned to 37°C for 3 h (particle size and count by microscopy on change in temperature). Depletion of Sam68 or HNRNPD by RNAi in HeLa cells in vivo resulted in the disappearance of SNBs as detected by immunofluorescence, whereas depletion of the three other proteins (HNRNPL, DBC1, and ZNF346) hardly affected the integrity of SNBs. The isoforms of HNRNPD containing exon 7 (p42 and p45) localize in SNBs and function in their formation. A coimmunoprecipitation-based detection assay with FLAG-tagged HNRNPD isoforms indicated that p42 and p45 physically interact with Sam68, HNRNPL, and DBC1. Based on Venus-p45 as the wild-type (WT) Venus-HNRNPD construct, two phenylalanine residues essential for RNA binding in each of RRM1 and RRM2 were mutated to aspartic acid to create mutants RRM1-M (F140D/F142D) and RRM2-M (F225D/F227D), which both failed to localize to SNBs, indicating that RNA binding of HNRNPD through the two RRMs simultaneously is essential for its SNB localization. RRM mutants also almost completely lacked the rescue activity for SNB formation. To examine whether the prion-like property of the HNRNPD prion-like domain is required for SNB formation, the tyrosine residues in the PLD of p45 were mutated to serine to create a partial Y-S mutant (nine tyrosine residues were altered) and a full Y-S mutant (all 18 Tyrs mutated). Both PLD Y-S mutants failed to localize to SNBs and showed significantly reduced rescue activity. FLAG-tagged PLD mutants neither interacted with Sam68 nor cotransfected Venus-tagged p45 itself (physical interaction by coimmunoprecipitation), indicating that the HNRNPD PLD is required for the interaction with Sam68 and for the homodimeric interaction of HNRNPD in SNBs. A substantial DBC1 signal was detected when an essential SNB component (protein localization), either Sam68 or HNRNPD, was knocked down. Furthermore, when HNRNPL was knocked down, the DBC1 signal was detected in nuclear foci distinct from those labeled with Sam68 and HNRNPD (protein localization). Both nuclear foci (the Sam68 substructure and the DBC1 substructure) were sensitive to RNase treatment (enzymatic activity assay). No in vitro results available, LLPS, formation of SNBs may require other factors (PMID:27377249). Confocal fluorescence microscopy of HeLa cells overexpressing N-terminally GFP- fused HNRNPD proteins in vivo showed localization HNRNPD into foci (protein localization), and disappearance of foci on the substitution of tyrosine residues to serines (PMID:28709000).
Experimental observations supporting the liquid material state of the condensate
temperature-dependence (PMID:27377249) reversibility of formation and dissolution (PMID:27377249)