LiteFold/DisProt huggingface dataset:
Protein: DP00519 (UniProt P25054)
Region: residues 1504	to 1528
Annotation: beta-catenin binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Phosphorylated R3 (pR3) was cocrystallized with the arm repeats of β-catenin at pH 6.5, and the structure solved at 2.1 Å. The final model contains β-catenin residues 150-550 and 559-664, and APC 1485-1499 and 1504-1528.
Cross-references: PDB:1V18
Protein: DP00519 (UniProt P25054)
Region: residues 1504	to 1528
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Phosphorylation results in the structuring of residues 1504-1528, which interact with β-catenin arm repeats 1-5 (Figures 3D and 3E).
Cross-references: PDB:1V18
Protein: DP00519 (UniProt P25054)
Region: residues 1504	to 1510
Annotation: phosphorylation display site (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Of the six phosphoserines present in the construct, those at positions 1504, 1505, 1507, and 1510, part of the consensus 1501SxxSSLSSLS APC 20-mer motif, are visible, and three of the four form direct contacts with β-catenin.
Cross-references: PDB:1V18
Protein: DP00519 (UniProt P25054)
Region: residues 1501	to 1510
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
APC is phosphorylated by GSK-3β and CK1ϵ (Rubinfeld et al. 1996, Rubinfeld et al. 2001). Mass spectrometry analysis of recombinant R3 treated with these two enzymes in vitro demonstrated that six serines are phosphorylated (data not shown).
Ser1505 is “primed” for CK1 phosphorylation by the presence of Asp1512 and Glu1513. Phosphorylated Ser1505 then serves as a priming site for GSK-3β-mediated phosphorylation of Ser1501. With Ser1501 phosphorylated, successive primed phosphorylations by CK1 can occur at Ser1504, Ser1507, and Ser1510. Phosphorylated Ser1507 can also prime a final phosphorylation of Ser1503 by GSK-3β. This scheme accounts for the presence of the six phosphates found in the mass spectroscopic analysis of in vitro-phosphorylated R3.
Cross-references: PDB:1V18
Protein: DP00531 (UniProt Q08655)
Region: residues 1	to 115
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of ASR1, without any additive, displayed a minimum dichroic peak cen- tered at 200 nm, typical of disordered conformations, and a low signal above 205 nm, charac- teristic of a more ordered structure (Fig 1A). These observations are in accordance with in silico predictions and experimental observations describing ASR1 as a disordered protein [8].
Protein: DP00531 (UniProt Q08655)
Region: residues 1	to 115
Annotation: disorder to order (Structural transition)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
We report that ASR1 adopts different conformations such as α-helix or polyproline type II in response to environ- mental changes. Low temperatures and low pH promote the polyproline type II conformation (PII). While NaCl increases PII content and slightly destabilizes α-helix conformation, PEG and glycerol have an important stabilizing effect of α-helix conformation.
Protein: DP00531 (UniProt Q08655)
Region: residues 1	to 115
Annotation: nucleic acid binding (Molecular function)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
The binding of Zn2 +in the low micromolar range promotes α-helix folding, while extra Zn2+ results in homo- dimerization. The ASR1-DNA binding is sequence specific and dependent on Zn2+.
Protein: DP00531 (UniProt Q08655)
Region: residues 1	to 115
Annotation: zinc ion binding (Molecular function)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Follow-
ing the CD signal change at 222 nm in the Zn2+ titration experiment and considering a 1:1
stoichiometry (see Materials and Methods), we estimated an equilibrium dissociation constant
between ASR1 and Zn2+, KZn2þ , of (9 ± 2) μM.
Protein: DP00531 (UniProt Q08655)
Region: residues 61	to 115
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Incubation of ASR1 with a variety of proteases resulted in the generation of a large number of low molecular weight proteolytic products (Fig. 4A). Binding of zinc to ASR1 induces conformational changes resulting in a decreased sensitivity to proteases.
Protein: DP00531 (UniProt Q08655)
Region: residues 61	to 115
Annotation: nucleic acid binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
South-western DNA- binding assays indicate that the carboxy-terminal domain of ASR1 containing residues 61–115 has a zinc-dependent DNA-binding activity, whereas the amino-terminal sequence (residues 1–60) does not (Fig. 1). Using mild acid hydrolysis, and a series of ASR1 carboxy-terminal truncations we show that the zinc-dependent DNA-binding could be mapped to the central/carboxy-terminal domain.
Protein: DP00539 (UniProt P51608)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 2. Circular dichroism spectra of MeCP2 domains reveal marked differences in secondary structure content. CD spectra are representative of two to four separate acquisitions. (a) Compared to the 195 nm peak indicative of β-sheet structure within the MBD (◼), all the other domains show a negative band in the 195−198 nm region indicative of disorder. NTD (●), TRD (○), and CTD-α (⊙) have lower structure content than ID (☆) and CTD-β (half-filled circles) (see Table 1 for quantitation)
To construct the NTD (residues 1−90), an amplicon extending 100 bp 5′ of the NdeI site into the pTYB1 vector sequence and carrying a 3′ EcoRI linker (GACCGTGAATTC) was generated by PCR from full-length pTYB1-MeCP2 cDNA carrying MeCP2 cDNA between its NdeI and EcoRI sites, using the following primer pairs: NTD Forward (5′ CCGGTTTAAACCGGGGATCTCGATCC 3′) and NTD Reverse (5′ GTTAGAGAATTCGTCACGGATGATGGAGCGCCGCTG 3′).
Protein: DP00539 (UniProt P51608)
Region: residues 207	to 310
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To construct the MBD (residues 75−164), ID (residues 165−210), TRD (residues 207−310), CTD-α (residues 261−330), and CTD-β (residues 335−486), we engineered amplicons with 5′ NdeI and 3′ EcoRI linkers
Figure 2. Circular dichroism spectra of MeCP2 domains reveal marked differences in secondary structure content. CD spectra are representative of two to four separate acquisitions. (a) Compared to the 195 nm peak indicative of β-sheet structure within the MBD (◼), all the other domains show a negative band in the 195−198 nm region indicative of disorder. NTD (●), TRD (○), and CTD-α (⊙) have lower structure content than ID (☆) and CTD-β (half-filled circles) (see Table 1 for quantitation)
Protein: DP00539 (UniProt P51608)
Region: residues 207	to 310
Annotation: nucleic acid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
From Table 1 the transcriptional repression domain (TRD) spans 207-310
The ID and TRD, when mixed with an equimolar amount of the 45 bp DNA substrate, resulted in striking changes in far-UV CD profiles, independent of the DNA methylation state (Figure 2b,c).
Protein: DP00539 (UniProt P51608)
Region: residues 165	to 210
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To construct the MBD (residues 75−164), ID (residues 165−210), TRD (residues 207−310), CTD-α (residues 261−330), and CTD-β (residues 335−486), we engineered amplicons with 5′ NdeI and 3′ EcoRI linkers
Figure 2. Circular dichroism spectra of MeCP2 domains reveal marked differences in secondary structure content. CD spectra are representative of two to four separate acquisitions. (a) Compared to the 195 nm peak indicative of β-sheet structure within the MBD (◼), all the other domains show a negative band in the 195−198 nm region indicative of disorder. NTD (●), TRD (○), and CTD-α (⊙) have lower structure content than ID (☆) and CTD-β (half-filled circles) (see Table 1 for quantitation).
Protein: DP00539 (UniProt P51608)
Region: residues 165	to 210
Annotation: molecular adaptor activity (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We also investigated interdomain associations intrans using CD, which can detect changes in secondary structure of one or both components in a mixture of the two (63).
With the NTD+MBD, MBD+ID, and MBD+TRD mixtures, we observed a clear difference between the summed individual CD spectra and the spectrum of an equimolar mixture (Figure 7b,c), indicating that an interaction between domains led to change(s) in secondary structure.
ID domain includes 165-210 residues
Protein: DP00539 (UniProt P51608)
Region: residues 335	to 486
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To construct the MBD (residues 75−164), ID (residues 165−210), TRD (residues 207−310), CTD-α (residues 261−330), and CTD-β (residues 335−486), we engineered amplicons with 5′ NdeI and 3′ EcoRI linkers
Figure 2. Circular dichroism spectra of MeCP2 domains reveal marked differences in secondary structure content. CD spectra are representative of two to four separate acquisitions. (a) Compared to the 195 nm peak indicative of β-sheet structure within the MBD (◼), all the other domains show a negative band in the 195−198 nm region indicative of disorder. NTD (●), TRD (○), and CTD-α (⊙) have lower structure content than ID (☆) and CTD-β (half-filled circles) (see Table 1 for quantitation).
Protein: DP00539 (UniProt P51608)
Region: residues 261	to 330
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To construct the MBD (residues 75−164), ID (residues 165−210), TRD (residues 207−310), CTD-α (residues 261−330), and CTD-β (residues 335−486), we engineered amplicons with 5′ NdeI and 3′ EcoRI linkers
Figure 2. Circular dichroism spectra of MeCP2 domains reveal marked differences in secondary structure content. CD spectra are representative of two to four separate acquisitions. (a) Compared to the 195 nm peak indicative of β-sheet structure within the MBD (◼), all the other domains show a negative band in the 195−198 nm region indicative of disorder. NTD (●), TRD (○), and CTD-α (⊙) have lower structure content than ID (☆) and CTD-β (half-filled circles) (see Table 1 for quantitation)
Of the six domains, the MBD was the only one showing a characteristic positive band in its CD spectrum at ∼197 nm, indicative of significant ordered secondary structure (Figure 2a). The others had a negative band in this region, indicating extensive disorder, with the NTD and TRD being the most strongly disordered
Protein: DP00539 (UniProt P51608)
Region: residues 165	to 210
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
(b) Addition of DNA (methylated as well as unmethylated) to the ID induces changes typical of the formation of β-structure, namely a marked increase in positive ellipticity at 195 nm and negative ellipticity in the 220−225 nm range.
Protein: DP00539 (UniProt P51608)
Region: residues 207	to 310
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
(c) Addition of DNA (methylated as well as unmethylated) to the TRD results in an increase in the level of order irrespective of the methylation status of the DNA.
Protein: DP00539 (UniProt P51608)
Region: residues 335	to 355
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The trypsin-resistant bands were excised from the gel and subjected to Edman sequencing. N-terminal sequences were obtained for bands 1-4 and band 6.
Even without positive identification of the C-terminal residues, it is apparent that the protease-resistant MeCP2 regions overlapped with the MBD, TRD, and C-terminal residues 355-486. Correspondingly, residues in the region between the MBD and TRD, as well as sites near residues 310 and 355, were relative hot spots for trypsin digestion.
Protein: DP00539 (UniProt P51608)
Region: residues 165	to 210
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The trypsin-resistant bands were excised from the gel and subjected to Edman sequencing. N-terminal sequences were obtained for bands 1-4 and band 6.
Even without positive identification of the C-terminal residues, it is apparent that the protease-resistant MeCP2 regions overlapped with the MBD, TRD, and C-terminal residues 355-486. Correspondingly, residues in the region between the MBD and TRD, as well as sites near residues 310 and 355, were relative hot spots for trypsin digestion.
Protein: DP00539 (UniProt P51608)
Region: residues 293	to 310
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The trypsin-resistant bands were excised from the gel and subjected to Edman sequencing. N-terminal sequences were obtained for bands 1-4 and band 6. The C-terminal ends of these bands could only be estimated from sizes returned by SDS-PAGE as we were unable to obtain masses from mass spectroscopy. These estimates took into account the anomalously high masses returned by SDS-PAGE.
Even without positive identification of the C-terminal residues, it is apparent that the protease-resistant MeCP2 regions overlapped with the MBD, TRD, and C-terminal residues 355-486. Correspondingly, residues in the region between the MBD and TRD, as well as sites near residues 310 and 355, were relative hot spots for trypsin digestion.
Protein: DP00539 (UniProt P51608)
Region: residues 168	to 486
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
We conducted droplet formation assays using physiologically relevant concentrations of recombinant MeCP2–GFP domain deletion mutant proteins in the presence of DNA. Although mutant proteins that lack the N-terminal IDR (ΔIDR-1) formed droplets, those that lack the C-terminal IDR (ΔIDR-2) did not (Fig. 2b–d). Furthermore, IDR-1 alone did not form droplets, whereas IDR-2 alone did—albeit with diminished size and number relative to both full-length and mutant ΔIDR-1 proteins (Fig. 2b–d).
MeCP2 full length (WT): residues 1-486; MeCP2 ΔIDR-1: residues 78-486; MeCP2 ΔIDR-2 (R168X): residues 1-167; MeCP2 IDR-1: residues 1-77; MeCP2 IDR-2: residues 168-486; MeCP2 ΔBasic: residues 1-486, removing IDR-2 basic patches (residues 170-181, 184-194, 246-258, 263-274, 282-289, 301-310, and 340-348); MeCP2 ΔAromatic: residues 1-486, removing IDR-2 aromatic residues (F226 and Y450); MeCP2 ΔHistidine: residues 1-486, removing IDR-2 histidine-rich domain (residues 366-372); MeCP2 ΔProline: residues 1-486, removing IDR-2 proline-rich domain (residues 376-405); MeCP2 R133C: residues 1-486, R133C; MeCP2 T158M: residues 1-486, T158M; MeCP2 P225R: residues 1-486, P225R MeCP2 R255X: residues 1-254; MeCP2 R270X: residues 1-269; MeCP2 R294X: residues 1-293; MeCP2 R306C: residues 1-486, R306C; MeCP2 P322L: residues 1-486, P322L; MeCP2 P389X: residues 1-288; MeCP2 Mini: as in the ΔNIC mutant from ref. 22.
Protein: DP00539 (UniProt P51608)
Region: residues 285	to 313
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
TBL1 WD40 domain was efficiently pulled down by wild-type NID but not by RTT mutant peptides or a peptide containing phosphoThr308, a modification known to interfere with NID binding (24) (Fig. 2C).
Protein: DP00539 (UniProt P51608)
Region: residues 285	to 313
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The R306C mutation was previously shown to disrupt an interaction between the MeCP2 NCoR-interaction domain (NID) and TBLR1—a subunit of the NCoR co-repressor complex13,21. We therefore examined the ability of R306C mutant condensates to incorporate the C-terminal domain of TBLR1 (TBLR1-CTD), which directly interacts with the NID21. Wild-type MeCP2 droplets readily enriched TBLR1-CTD–mCherry, whereas R306C mutant droplets showed less enrichment (Extended Data Fig. 7), which suggests that MeCP2 condensates can contribute to NID-mediated recruitment of NCoR, a key MeCP2 function previously shown to be disrupted in Rett syndrome13,21. These results suggest that missense mutations in IDR-2 that occur in patients with Rett syndrome contribute to condensate disruption.
Protein: DP00539 (UniProt P51608)
Region: residues 285	to 309
Annotation: protein binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Here, we show that the “NCoR/SMRT interaction domain” (NID) of MeCP2 directly contacts transducin beta-like 1 (TBL1) and TBL1 related (TBLR1), two paralogs that are core components of NCoR/SMRT. We determine the cocrystal structure of the MeCP2 NID in complex with the WD40 domain of TBLR1 and confirm by in vitro and ex vivo assays that mutation of interacting residues of TBLR1 and TBL1 disrupts binding to MeCP2.
Fluorescence anisotropy binding with a minimal 11-mer peptide of MeCP2 (residues 298–309). Anisotropy is measured in arbitrary units (A.U.).
Protein: DP00539 (UniProt P51608)
Region: residues 285	to 309
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Using surface plasmon resonance (SPR), we measured binding constants (KDs) for alternative NID peptides (NIDs, residues 285–309; or NID, residues 285–313) with the mouse TBLR1-CTD (residues 134–514) (Fig. 2D and Fig. S2B). Wild-type TBLR1-CTD bound MeCP2 NID and MeCP2 NIDS with apparent KDs of 9.5 ± 0.5 μM and 12.9 ± 0.8 μM, respectively.
Protein: DP00539 (UniProt P51608)
Region: residues 207	to 310
Annotation: nucleic acid binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Among the individual domains, the NTD and CTD-β stand out as inducing only very minor mobility shifts in DNA, whereas the ID, TRD, and CTD-α fragments all induce marked shifts (Figure 3a).
From table 1 TRD spans 207-310
Protein: DP00543 (UniProt Q14061)
Region: residues 1	to 63
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectra of reduced hCox17 displays much
lower ellipticity and a minimum at 205 nm consistent with a mostly disordered structure. This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00543 (UniProt Q14061)
Region: residues 25	to 60
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectra of reduced hCox17 displays much
lower ellipticity and a minimum at 205 nm consistent with a mostly disordered structure. This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00543 (UniProt Q14061)
Region: residues 25	to 60
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV circular dichroism (CD) of native hCox17 is typical of an α-helix containing protein. The far-UV CD spectra of reduced hCox17 displays much
lower ellipticity and a minimum at 205 nm consistent with a mostly disordered structure.
Protein: DP00543 (UniProt Q14061)
Region: residues 1	to 63
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00543 (UniProt Q14061)
Region: residues 25	to 60
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00543 (UniProt Q14061)
Region: residues 25	to 60
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The spectra of the reduced form is typical to disordered protein while the oxidized one is more heterogeneious, like for globular protein.
Protein: DP00543 (UniProt Q14061)
Region: residues 1	to 63
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00543 (UniProt Q14061)
Region: residues 25	to 63
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00543 (UniProt Q14061)
Region: residues 25	to 63
Annotation: disorder to order (Structural transition)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Tese results agree with the Fourier transform infrared spectroscopy (FTIR) spectrum of DTT treated hCox17 in the amide I region, which evidences the lack of signifcant regular secondary structure, whereas the FTIR of spectrum of native hCox17 contains a 44% α-helical content.
Protein: DP00543 (UniProt Q14061)
Region: residues 1	to 63
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This lack of structural transition is in agreement with the NMR and FTIR data, supporting hCox17 being mostly disordered in the reduced state.
Protein: DP00553 (UniProt Q9NZ94)
Region: residues 731	to 848
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Abnormal migration of the full-length hNL3-cyt domain on SDS-PAGE, as well as CD analysis of the heterogeneous hNL3-cyt solution in the far UV (Fig. S3 in Data S1), both provided early indications that hNL3-cyt is an IUP.
 All three spectra lack any major contributions from α-helices, β-sheets or turns, and are characteristic of an unstructured polypeptide, with a possible PPII contribution (36,70,71).
Protein: DP00553 (UniProt Q9NZ94)
Region: residues 731	to 848
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
hNL3-cyt displays a shape typical of unfolded proteins, i.e., a plateau that increases monotonically at higher s values, whereas that for BSA displays a bell-shaped Kratky plot (Fig. 9 C).