LiteFold/DisProt huggingface dataset:
Protein: DP04308 (UniProt P43586)
Region: residues 1	to 204
Annotation: rRNA binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
In order to assess the cellular binding targets of Loc1p, we immunoprecipitated TAP-tagged Loc1p expressed in yeast under the endogenous promoter and identified the co-purified RNAs by cDNA microarrays. Among the co-purified RNAs, the class of rRNAs was highly enriched (Supplementary Figure S1A and Supplementary Tables S2 and S3), suggesting that this nucleolar RNA-binding protein preferentially binds to rRNAs.
The interaction with both pro- and eukaryotic ribosomes suggests unspecific binding to rRNA or ribosomal proteins and a rather general mode of ribosome association.
Furthermore, Loc1p stabilizes the energetically most favored conformation of E3 in a time-course experiment with molecular beacons and antisense RNA strands (Supplementary Figure S6B).
Loc1p forms condensates with a 28nt E3 localization element (LE) of ASH1 mRNA and promotes conformational changes in its stem-loop.
Protein: DP04308 (UniProt P43586)
Region: residues 1	to 204
Annotation: RNA folding chaperone (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
To assess this possibility, we performed in vitro RNA chaperone experiments with a 27-base stem–loop labeled at its 5′-end with a fluorescent dye and at its 3′-end with a quencher molecule (22,57). 
In contrast, in the presence of Loc1p we observed an ∼7-fold increased reaction rate toward the formation of the energetically favored dsRNA (Figure ​2C, right panel). Thus, similarly to a catalytic reaction, Loc1p accelerates the transition of folded RNAs toward their thermodynamically most favored state.
Protein: DP04308 (UniProt P43586)
Region: residues 1	to 204
Annotation: RNA strand annealing activity (Molecular function)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
In this assay, Loc1p showed by far the strongest annealing activity of all tested chaperones (Figure ​2D).
Thus, under these experimental conditions, Loc1p was the most potent nucleic acid annealing catalyst among the tested chaperones.
Loc1p (1–20)10 showed again a >50-fold improvement in activity over Loc1p (1–20)2 (Figure ​4G and H). These findings suggest that the RNA-binding motifs in Loc1p act cooperatively in nucleic acid annealing. Interestingly, wild-type Loc1p and Loc1p (1–20)10 showed comparable activities in this assay (Figure ​4G), suggesting that the concatenation of PUN motifs is sufficient to achieve wild-type annealing activity.
Protein: DP04308 (UniProt P43586)
Region: residues 1	to 204
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
We first mixed increasing amounts of recombinant Loc1p with 0.5× mass ratio of total HeLa cell RNA and observed formation of microscopically visible condensates at Loc1p concentrations of 5 μM or higher (Figure ​(Figure5A).5A). The number and size of the condensates were clearly dependent on the Loc1p concentration, while 30 μM Loc1p without RNA did not result in phase separation.
Notably, formation of liquid-liquid phase separations (LLPS) with an in vitro transcribed 28-nt-long E3 (21) is observed for Loc1p concentrations >5 μM but not in the absence of RNA (Supplementary Figure S6A).
Protein: DP04308 (UniProt P43586)
Region: residues 1	to 204
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
Fluorescence of Cy5-Loc1pS7C/RNA condensates recovered after photobleaching on average to 20–30% after 30 s (Figure ​(Figure5E5E and Supplementary Movie S2), demonstrating a dynamic exchange of Loc1p between the droplets and the surrounding protein solution. Both the droplet fusion and the fluorescence recovery to around 20–30% are in line with the assumption that the observed condensates have liquid-like to gel-like properties.
Protein: DP04308 (UniProt P43586)
Region: residues 1	to 20
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Indeed, Loc1p (1–20)10 formed visible condensates already at a concentration of 2.5 μM protein and a mass ratio of 0.025× RNA (Figure ​5F). We further confirmed the robustness of the apparent PUN motif-mediated phase separation by providing a constant concentration of Loc1p (1–20)10 and increasing ratios of RNA (Figure ​5G). In all cases, RNA-dependent phase separation was observed.
Protein: DP04309 (UniProt Q9UJY1)
Region: residues 1	to 89
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
According to “double wavelength” plot, [θ]222 vs [θ]200, proposed by Uversky [13], the CD spectrum of Hsp22 roughly, but not entirely, corresponds to that of a protein in the pre-molten-globule-like state. These CD data indicate that the structure of Hsp22 is more ordered than that typical for proteins in the pre-molten-globule-like state.
The data of FTIR indicate that at 20 °C Hsp22 contains about 33% of β-sheets, about 12% of α-helices, about 34% of turns, and about 21% disordered random-coil structures. This estimation correlates well with the corresponding data obtained earlier by CD spectroscopy [9]. According to predictions, almost all β-strands of Hsp22 are located in the α-crystallin domain, while α-helices are mainly localized in the N-terminal part of the molecule [10].
These DSC data unambiguously indicate that at low temperature a significant portion of the Hsp22 molecule lacks rigid tertiary structure and therefore possesses properties of intrinsically disordered proteins. 
This conclusion agrees with the prediction of disordered regions in Hsp22 [10] indicating that three Trp residues are located in presumably unordered regions and only Trp96 is located in a more or less ordered region (residues 90–120 of α-crystallin domain).
According to the predictions of a structural disorder, it was assumed that Hsp22 belongs to the growing family of intrinsically disordered proteins (IDP), although some parts of its molecule are more or less ordered (residues 90–120 and 140–170 in the α-crystallin domain) [10].
The combination of experimental evidences and prediction approaches let us determine this region as intrinsically disordered.
Protein: DP04309 (UniProt Q9UJY1)
Region: residues 171	to 196
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
According to “double wavelength” plot, [θ]222 vs [θ]200, proposed by Uversky [13], the CD spectrum of Hsp22 roughly, but not entirely, corresponds to that of a protein in the pre-molten-globule-like state. These CD data indicate that the structure of Hsp22 is more ordered than that typical for proteins in the pre-molten-globule-like state.
This conclusion agrees with the prediction of disordered regions in Hsp22 [10] indicating that three Trp residues are located in presumably unordered regions and only Trp96 is located in a more or less ordered region (residues 90–120 of α-crystallin domain).
These DSC data unambiguously indicate that at low temperature a significant portion of the Hsp22 molecule lacks rigid tertiary structure and therefore possesses properties of intrinsically disordered proteins.
The data of FTIR indicate that at 20 °C Hsp22 contains about 33% of β-sheets, about 12% of α-helices, about 34% of turns, and about 21% disordered random-coil structures. This estimation correlates well with the corresponding data obtained earlier by CD spectroscopy [9]. According to predictions, almost all β-strands of Hsp22 are located in the α-crystallin domain, while α-helices are mainly localized in the N-terminal part of the molecule [10].
According to the predictions of a structural disorder, it was assumed that Hsp22 belongs to the growing family of intrinsically disordered proteins (IDP), although some parts of its molecule are more or less ordered (residues 90–120 and 140–170 in the α-crystallin domain) [10].
The combination of experimental evidences and prediction approaches let us determine this region as intrinsically disordered.
Protein: DP04324 (UniProt Q969S2)
Region: residues 56	to 129
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
For example, amino acid residues 37–55 and 238–265 demonstrated essentially no exchange in the first 10 s, whereas residues 56–129 from the prolinerich region showed the largest deuterium uptake of 65%.
The full time course of H/D exchange events for each peptide is illustrated by the butterfly plot in Figure 3(A). It can be seen that the amide hydrogens of residues 56–129 exchange fast and reach the maximum of saturation within the first ten seconds, which is consistent with the behavior of unstructured regions.
Protein: DP04325 (UniProt O95714)
Region: residues 4793	to 4834
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In contrast, the 15N‐HSQC spectrum for the HERC2 negatively charged C‐terminal tail showed that this region is disordered as indicated by the narrow distribution of amide peaks (Figure 5a).
Protein: DP04325 (UniProt O95714)
Region: residues 4793	to 4834
Annotation: flexible C-terminal tail (Disorder function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
To determine their biological relevance, a 15N‐HSQC spectrum was collected for the HERC2 extended C‐lobe (residues G4676–H4834). When this spectrum was overlaid with the 15N‐HSQC spectra for the isolated HERC2 C‐lobe and negatively charged C‐terminal tail, there was a significant amount of peak overlap (Figure 6). These data show that the isolated HERC2 C‐lobe and negatively charged C‐terminal tail constructs are biologically relevant since the chemical environment of most residues was not significantly different when compared the HERC2 extended C‐lobe spectrum.
Protein: DP04325 (UniProt O95714)
Region: residues 4793	to 4834
Annotation: flexible C-terminal tail (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectra and normalized melting curves indicate that the HERC2 negatively charged C‐terminal tail increases the stability of the HERC2 C‐lobe.
Protein: DP04325 (UniProt O95714)
Region: residues 4793	to 4834
Annotation: protein stabilization (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectra and normalized melting curves indicate that the HERC2 negatively charged C‐terminal tail increases the stability of the HERC2 C‐lobe.
Protein: DP04328 (UniProt P32833)
Region: residues 1	to 232
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of S. cerevisiae ORC bound to 84 bp ARS1 DNA shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7TJF
EMDB:25924
Protein: DP04328 (UniProt P32833)
Region: residues 344	to 354
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of S. cerevisiae ORC bound to 84 bp ARS1 DNA shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7TJF
EMDB:25924
Protein: DP04328 (UniProt P32833)
Region: residues 498	to 620
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structures of S. cerevisiae ORC bound to 84 bp ARS1 DNA shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7TJF
EMDB:25924
Protein: DP04328 (UniProt P32833)
Region: residues 176	to 200
Annotation: chromatin binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
We found that both Cdt1-Mcm2-7 and OCCM can be pulled down by GST-Orc2N200, but not by GST-Orc2N175 or GST alone (Fig. 5a, b), indicating a direct interaction between Orc2-SH(175-200) and Mcm2-7 containing complexes.
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: nuclear membrane biogenesis (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Such abnormal vacuoles in the nucleus were located in close proximity to the NE, which is rich in nuclear pore complexes (NPCs) (Fig. 2H, asterisks and Fig. S4 for serial sectioning images). Notably, the nuclear protein did not leak out of the nucleus (Fig. S5), indicating that the NE retained its function as a barrier between the nucleus and the cytoplasm despite its abnormal morphology. The electron-dense patches were distributed over a wide area within the nucleoplasm but were scarcely distributed in the nucleolus (see serial sectioning images in Fig. S4B). Patches were observed in 45 of 50 nuclei overexpressing IDR. 
The atypical structures observed under live fluorescence imaging (Fig. 2E) were preserved without any obvious alterations during fixation for CLEM (Fig. S4A). We found two major abnormalities: a vacuole-like structure covered with a multilayered membrane within the nucleus, and electron-dense patches in the nucleoplasm (Fig. 2H, red and blue arrows, respectively), both of which were not observed in wild-type cells (Fig. 2I).
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: chromosome organization (Biological process)
Evidence: over expression analysis evidence used in manual assertion
Supporting statements:
Overexpression of the GFP-IDR and GFP-IDR-TM fragments, but not GFP and GFP-KSE, caused dissociation of the centromeres from the NE and their declustering (Fig. 3, A and B).
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: lipid binding (Molecular function)
Evidence: lipid binding assay evidence used in manual assertion
Supporting statements:
In this study, we focused on PA in the following experiments because the abnormal membrane proliferation observed with Bqt4 overexpression was similar to that observed in the ned1-deficient phenotype. To confirm the binding of PA to the IDR, we performed a liposome-mediated binding assay. Liposomes with different percentages of PA were prepared and incubated with purified GFP-IDR protein. After isolation of the liposomes via density gradient centrifugation, the proteins bound to the liposomes were electrophoresed and detected using silver staining. GFP-IDR co-sedimented with PA-containing liposomes but not with control liposomes (Fig. 4B). Therefore, we conclude that the IDR region directly binds to PA in vitro.
Because PA and cardiolipin are negatively charged lipids (Fig. 4A), and the IDR region, especially the KSE region, is biased toward a positive charge (Fig. 4C), we assumed that the interaction between PA and the IDR region is mediated via electrostatic interactions.
Protein: DP04337 (UniProt O60158)
Region: residues 372	to 377
Annotation: lipid binding (Molecular function)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
The FRAP analysis revealed that GFP-ΔKSE and GFP-4KRA moved faster than full-length Bqt4 (GFP-FL) in the INM, suggesting that Bqt4 forms a sub-stable complex with the INM by interacting with PA. To further confirm the electrostatic interaction between the IDR and PA, we generated mutants by scrambling and reversing the amino acid sequences in the KSE region to disturb its electrostatic potential (Fig. S7A).
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Purified GFP-IDR protein was mixed with an increased concentration of PA, and the mixture was observed using fluorescence microscopy. As shown in Figure 5, A and B, GFP-IDR formed fibrous aggregates in a PA-dependent manner. Consistent with the lipid binding assay results, aggregates were not formed with the neutral phospholipid phosphatidylcholine (PC).
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence correlation spectroscopy evidence
Supporting statements:
To further assess the aggregation state of GFP-IDR, we performed FCS analysis. In the presence of PA, fluorescence intensity fluctuations of approximately 100 kHz were accompanied by strong spike signals for the GFP-IDR (Fig. S9A), most likely originating from large fibrous aggregates observed in Figure 5, A and B passing through the confocal volume. Conversely, in the absence of PA, fluctuations were less than 10 kHz (Fig. S9A, compare inlets for GFP-IDR+PA and control), a range similar to that observed when using GFP instead of GFP-IDR, or PC instead of PA (Fig. S9A). The auto-correlation function (G(τ)), calculated from these fluctuations, showed that GFP-IDR exhibits slower diffusion with PA compared to other combinations (Fig. 5C). These results suggest that GFP-IDR formed microscopically invisible clusters with PA, in addition to large visible aggregates. As the large aggregates were not spherical, they are unlikely to have been formed by liquid-liquid phase separation. We also performed an FRAP assay on GFP-IDR within the aggregates and found that its molecular exchange rate was low (Fig. 5D), suggesting that the aggregates are of a solid phase, not a liquid phase. Collectively, the IDR tended to form a cluster in the presence of PA; ultimately, this cluster transitioned into a large, solid, fibrous aggregate in vitro.
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: disorder (Structural state)
Evidence: author inference based on intrinsic disorder prediction used in manual assertion
Supporting statements:
For this purpose, we examined the three-dimensional protein structure around the KSE domain predicted by Alphafold2 (https://alphafold.ebi.ac.uk/entry/O60158) and selected an unstructured region (364–413 aa; Fig. 2A) containing the KSE domain as a candidate. We termed this region as an intrinsically disordered region.
 From this prediction, we examined the 340 to 383 aa region which consists of α-helix (340–363 aa) and low complex regions (364–383 aa) (Fig. 1D and red and blue squared regions in Fig. S1A).
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 383
Annotation: nuclear membrane organization (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Upon thiamine addition, GFP–GST–NLS severely leaked from the nucleus of ΔKSE mutant-expressing cells, but not from the nucleus of FL-expressing cells (Fig. 1, G and H), indicating NE rupture in the ΔKSE mutant-expressing cells. These results suggest that the KSE domain is vital for NE maintenance.
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: nuclear envelope (Cellular component)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
The IDR fragment of Bqt4 tagged with GFP (GFP-IDR) was localized to the NE despite the absence of TM and nucleoplasm under suppressive expression conditions (Fig. 2B, +thiamine).
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: nuclear envelope organization (Biological process)
Evidence: over expression analysis evidence used in manual assertion
Supporting statements:
When GFP-IDR was overexpressed in S. pombe cells under the control of the nmt1 promoter, its overexpression resulted in severe growth defects in the spot assay (Fig. 2D). These results indicate that the overexpression of IDR, but not KSE, confers dominant-negative effects on cell growth and suggest that the IDR domain is substantial for NE maintenance, causing loss-of-function and dominant-negative effects.
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: centromere clustering at the mitotic interphase nuclear envelope (Biological process)
Evidence: over expression analysis evidence used in manual assertion
Supporting statements:
Overexpression of the GFP-IDR and GFP-IDR-TM fragments, but not GFP and GFP-KSE, caused dissociation of the centromeres from the NE and their declustering (Fig. 3, A and B).
Time-lapse observation of the cells overexpressing IDR-TM revealed that aberrant nuclear membrane expansion occurred just after mitosis; subsequently, the clustered centromeres started to dissociate from the NE and then declustered (Fig. 3C and Movie S1). Consequently, the chromosome was missegregated during the next mitosis (Fig. 3C).
Overexpression of the IDR region disturbs centromere clustering.
Protein: DP04337 (UniProt O60158)
Region: residues 364	to 413
Annotation: regulation of membrane lipid distribution (Biological process)
Evidence: over expression analysis evidence used in manual assertion
Supporting statements:
 These results suggested that Bqt4 collects PA-enriched membranes to the NE via its IDR domain. In IDR-overexpressing cells, GFP-IDR was localized in both the nucleoplasm and cytoplasm (Fig. 6A, IDR). Consequently, the PA sensor was redistributed from the nucleus to the cytoplasm (Fig. 6A; IDR). In contrast, KSE overexpression did not alter the localization of the PA sensor, although this fragment was localized in the cytoplasm, similar to IDR (Fig. 6A, KSE). Therefore, we conclude that IDR, but not KSE, controls intracellular PA localization depending on its localization and protein levels in S. pombe cells. 
Overexpression of IDR disturbs intracellular lipid distribution.
Protein: DP04340 (UniProt P17433)
Region: residues 1	to 170
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal regions of both proteins that are involved in interactions with other factors are intrinsically disordered26,27.
The Cryo-EM structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:8EVH
EMDB:28629
Protein: DP04340 (UniProt P17433)
Region: residues 260	to 272
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal regions of both proteins that are involved in interactions with other factors are intrinsically disordered26,27.
The Cryo-EM structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:8EVH
EMDB:28629
Protein: DP04341 (UniProt P08551)
Region: residues 440	to 543
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS measurements of WT and ΔN42 at different salinity (Cs). a For increasing Cs, the WT variant shows increased small-angle scattering, a signature for aggregation. In contrast, ΔN42 remains structurally intrinsically disordered as Cs vary.
The ΔN42 variant remains disordered and unchanged with salinity, while the WT variant shows a hump at low q, typical for a collapse region. 
In contrast, ΔN42 shows a separated Gaussian polymer profile (Figs. 1a, S1), nearly insensitive to total salinity (Cs=20-520 mM). Similarly, the data presented in Kratky format (qI2 vs. q, Fig. 1a) show the ΔN42 has the signature of a disordered polymer.