LiteFold/DisProt huggingface dataset:
Protein: DP00506 (UniProt P07766)
Region: residues 1	to 32
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the structure of human T cell receptor-CD3 complex shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:6JXR
Protein: DP00506 (UniProt P07766)
Region: residues 157	to 207
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the structure of human T cell receptor-CD3 complex shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:6JXR
Protein: DP00508 (UniProt P09693)
Region: residues 139	to 182
Annotation: self-assembly (Disorder function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The gel filtration data indicated that there exists a fast dynamic equilibrium between monomeric and dimeric cytoplasmic domains of all of the ITAM-containing proteins studied, again with the exception of Igαcyt (see below).
Protein: DP00508 (UniProt P09693)
Region: residues 139	to 182
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD analysis of CD3εcyt, CD3δcyt, CD3γcyt, FcεRIγcyt, Igαcyt, and Igβcyt showed that these proteins are unstructured, random-coiled proteins. In each case, no detectable secondary or tertiary structure was observed with increasing protein concentration (data not shown).
Protein: DP00508 (UniProt P09693)
Region: residues 1	to 23
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the structure of human T cell receptor-CD3 complex shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:6JXR
Protein: DP00508 (UniProt P09693)
Region: residues 139	to 182
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the structure of human T cell receptor-CD3 complex shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:6JXR
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of hp8 at pH 6.0 and 25 °C displays an intense minimum at 205 nm (Fig.3 A) and a shoulder expanding from 220 to 230 nm. Such spectrum resembles, except for the shoulder, that of a random coil structure (17, 18).
The percentage of calculated structure is 2%. Thus, hp8 from the far-UV spectra is mainly random coil.
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Fig. 10 B shows that DNA binding activity was increased when hp8 recombinant protein was previously phosphorylated by PKA catalytic subunit. A rough estimate of 7-fold increase in affinity can be calculated from the increase in intensity of the complex at similar concentrations of hp8 and PKAhp8 proteins (around 2-fold) and the degree of phosphorylation of PKAhp8, which is around 30% (see before).
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The infrared spectrum of nonphosphorylated hp8 (Fig. 4 A) showed an amide I band with a maximum centered near 1644 cm−1, which is characteristic of nonordered conformations.
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: phosphorylation display site (Disorder function)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
When using unlabeled ATP, protein phosphorylation was checked by observing the 950–1300 cm−1 band of the FTIR spectra (25).
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
The near-UV signal of hp8 was null at pH 6.0 and did not change with either the pH or temperature, suggesting the absence of a well fixed structure.
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The lack of a well fixed tertiary structure was also confirmed by fluorescence studies. The fluorescence spectrum of hp8 shows exposed tyrosine residues, with a maximum at 305 nm (data not shown).
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: heat capacity-based evidence used in manual assertion
Supporting statements:
The lack of a well fixed tertiary structure was also confirmed by fluorescence studies. The fluorescence spectrum of hp8 shows exposed tyrosine residues, with a maximum at 305 nm (data not shown).
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The one-dimensional NMR spectra of human hp8 at 5 °C showed small chemical shift dispersion: the amide (Fig. 5 A,left) and the methyl (Fig. 5 A, right) protons were clustered in those regions expected for random coil proteins (24).
Furthermore, the two-dimensional nuclear Overhauser effect spectroscopy experiments showed lack of long-range contacts (data not shown), suggesting the absence of a well fixed tertiary structure.
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: DNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum obtained after incubation of PKAhp8 and DNA together was different from that obtained by adding the spectra of both molecules separately.
 At 222 nm, the added spectrum showed a more negative ellipticity than that of the complex; conversely, in the region ranging from 225 to 240 nm, the spectrum of the complex showed a lower intensity than that of the added spectrum. These changes suggest that PKAhp8 binds DNA.
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: phosphorylation display site (Disorder function)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
The fact that hp8 has a high percentage of serines and threonines prompted us to assay the capacity of being phosphorylated by some of the protein kinases predicted to have putative target sites in hp8. Fig. 6 shows that protein kinase A (PKA) and casein kinase 2 phosphorylated hp8, but that Cdc2k did not.
Protein: DP00510 (UniProt O60356)
Region: residues 1	to 82
Annotation: phosphorylation display site (Disorder function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Even at highly optimized phosphorylation conditions, only 30% of hp8 could be phosphorylated, assuming that one phosphate was incorporated per molecule; phosphorylation produced the typical shift in electrophoretic mobility of phosphorylated proteins (Fig. 7).
Protein: DP00512 (UniProt P56210)
Region: residues 77	to 87
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
There are, however, two exceptions to this generalization: the six N-terminal residues and residues I20 to N30 in loop 1 both exhibit considerable disorder over the ensemble of calculated structures (Figure 5(a)).
Cross-references: PDB:2FOW
PDB:1FOY
Protein: DP00512 (UniProt P56210)
Region: residues 77	to 87
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, these data indicate that loop 1 becomes ordered upon binding to its cognate RNA.
Protein: DP00512 (UniProt P56210)
Region: residues 76	to 91
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although the structure can be considered high resolution in the core, 15 residues between helix α1 and strand β1 form an extended, unstructured loop.
Cross-references: PDB:1FOX
PDB:1FOW
Protein: DP00512 (UniProt P56210)
Region: residues 76	to 91
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For L11-C76, the loop between α1 and β1 shows the most striking change in chemical shifts upon binding; for the homeodomain complex, only one contact to the phosphate backbone is made by the loop between helix 1 and helix 2.
Protein: DP00512 (UniProt P56210)
Region: residues 77	to 87
Annotation: rRNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The other protein residues that have NOEs to the RNA are S24, E26, and P27 in loop 1. Thus, residues located near the center of loop 1 associate intimately with target RNA. Moreover, the dramatic loop 1 structural and dynamic changes detailed earlier, appear to be the direct result of the interaction of L11-C76 with its target RNA, not merely an indirect structural/dynamic change that accompanies RNA binding.
Protein: DP00512 (UniProt P56210)
Region: residues 76	to 91
Annotation: rRNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The flexible loop is important for RNA binding
Chemical shifts differences between the free protein and the bound protein suggest that the loop as well as the C-terminal end of helix α3 are involved in RNA binding.
Protein: DP00519 (UniProt P25054)
Region: residues 1362	to 1745
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In addition, our CD and NMR studies demonstrate that the central region of APC is unstructured in the absence of beta-catenin and Axin, and suggest that beta-catenin may interact with each of the APC 15aa and 20aa repeats independently.
To determine if the central region of APC has a defined secondary structure, the CD spectra of various purified APC fragments, including APC-R2-R3 and APC-R2-R4, were measured. The CD spectra measured for APC-R2-R4 at 4 °C and 25 °C are essentially identical and feature a single minimum in molar residue ellipticity at ∼200 nm (Figure 3(b)). These spectra, as well as the CD spectra for other APC fragments (data not shown), indicate that all these APC fragments are mostly unstructured.
Protein: DP00519 (UniProt P25054)
Region: residues 1362	to 1745
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In addition, our CD and NMR studies demonstrate that the central region of APC is unstructured in the absence of beta-catenin and Axin, and suggest that beta-catenin may interact with each of the APC 15aa and 20aa repeats independently.
To exclude the possibility that the APC fragment has a defined structure without regular secondary structure, we measured both 1D and 2D NMR spectra of APC-R2-R4, the longest APC fragment that we were able to obtain in large quantity and that has good solubility. 1D NMR shows no obvious chemical shift signal from 5.5 ppm to 8.5 ppm. The poor dispersion of the resonances indicates that the fragment does not have a folded structure (Figure 3(c)). This lack of folded conformation is also demonstrated in the 2D Nuclear Overhauser Effect (NOE) spectra; there is no inter-residue NOE observed in the 2D-NOESY spectrum, which is characteristic of an unfolded structure (data not shown).
Protein: DP00519 (UniProt P25054)
Region: residues 2781	to 2819
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The effect of phosphorylation at these sites on binding to the C-terminal domain of EB1 (EB1c) was assessed in vitro by isothermal titration calorimetry (ITC) with a polypeptide corresponding to the sequence of APC39 (APCp1; Bu and Su, 2003, Honnappa et al., 2005). ITC revealed that two APCp1 peptides bind to one EB1c dimer, with an equilibrium dissociation constant, Kd, of 5.8 ± 0.1 μM (Figure S5), consistent with previous findings (Honnappa et al., 2005). Peptides phosphorylated at Ser2789 (Honnappa et al., 2005) or Ser2793 (Figure S5) showed ∼4- and ∼6-fold reduced affinity for EB1c when compared to the wild-type peptide.
Cross-references: ELM:LIG_SxIP_EBH_1
Protein: DP00519 (UniProt P25054)
Region: residues 2803	to 2809
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In order to determine whether the structural features observed in the EB1cΔC8-MACFp1 complex apply more generally to EB1-mediated +TIP interactions, we performed nuclear magnetic resonance (NMR) experiments on the EB1c-APCp1 complex. 15N{1H}-NOEs demonstrate that whereas APCp1 is unstructured in solution (not shown), the segment 2784–2813 is ordered in the complex with EB1c (Figure 6A). Chemical shift changes and intermolecular 1H-1H NOEs identify residues 2803–2809 encompassing the SxIP motif as a major interaction site, with secondary interactions at residues 2789–2799 (Figure 6A; Figure S7). The remainder of the APCp1 polypeptide is disordered even in the bound state.
Protein: DP00519 (UniProt P25054)
Region: residues 2789	to 2799
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In order to determine whether the structural features observed in the EB1cΔC8-MACFp1 complex apply more generally to EB1-mediated +TIP interactions, we performed nuclear magnetic resonance (NMR) experiments on the EB1c-APCp1 complex. 15N{1H}-NOEs demonstrate that whereas APCp1 is unstructured in solution (not shown), the segment 2784–2813 is ordered in the complex with EB1c (Figure 6A). Chemical shift changes and intermolecular 1H-1H NOEs identify residues 2803–2809 encompassing the SxIP motif as a major interaction site, with secondary interactions at residues 2789–2799 (Figure 6A; Figure S7). The remainder of the APCp1 polypeptide is disordered even in the bound state.
Protein: DP00519 (UniProt P25054)
Region: residues 2781	to 2819
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In order to determine whether the structural features observed in the EB1cΔC8-MACFp1 complex apply more generally to EB1-mediated +TIP interactions, we performed nuclear magnetic resonance (NMR) experiments on the EB1c-APCp1 complex. 15N{1H}-NOEs demonstrate that whereas APCp1 is unstructured in solution (not shown), the segment 2784–2813 is ordered in the complex with EB1c (Figure 6A). Chemical shift changes and intermolecular 1H-1H NOEs identify residues 2803–2809 encompassing the SxIP motif as a major interaction site, with secondary interactions at residues 2789–2799 (Figure 6A; Figure S7). The remainder of the APCp1 polypeptide is disordered even in the bound state.
APCp1 corresponds to region Val2781-Lys2819 of human APC.
Protein: DP00519 (UniProt P25054)
Region: residues 2784	to 2813
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In order to determine whether the structural features observed in the EB1cΔC8-MACFp1 complex apply more generally to EB1-mediated +TIP interactions, we performed nuclear magnetic resonance (NMR) experiments on the EB1c-APCp1 complex. 15N{1H}-NOEs demonstrate that whereas APCp1 is unstructured in solution (not shown), the segment 2784–2813 is ordered in the complex with EB1c (Figure 6A). Chemical shift changes and intermolecular 1H-1H NOEs identify residues 2803–2809 encompassing the SxIP motif as a major interaction site, with secondary interactions at residues 2789–2799 (Figure 6A; Figure S7). The remainder of the APCp1 polypeptide is disordered even in the bound state.
APCp1 corresponds to region Val2781-Lys2819 of human APC.
Protein: DP00519 (UniProt P25054)
Region: residues 1459	to 1532
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Despite the sequence homology, each of the seven 20aa repeats binds to β-catenin with dramatically different affinities. When unphosphorylated, APC-R3 can bind β-catenin with a Kd of ∼0.2 μM. The binding of β-catenin with every other unphosphorylated 20aa repeat is at least 60 times weaker than APC-R3, and unlikely to interact with β-catenin at physiological conditions (see Discussion).
However, APC-R3 is obviously the repeat having the highest affinity with β-catenin in both phosphorylated and unphosphorylated states.
The APC-rBC fragment interacts with two β-catenin molecules, indicating each 15aa repeat binds to one β-catenin molecule. In addition, APC-R2-R4 also interacts with two molecules of β-catenin, indicating that both APC-R3 and APC-R4, but not APC-R2, interact with one molecule of β-catenin simutaneously (Table 1). Thus our ITC study confirms the binding stoichiometry of one β-catenin binding repeat of APC to one β-catenin molecule.
This region corresponds to APC repeat 3 (APC-R3, residues 1459–1532).
Protein: DP00519 (UniProt P25054)
Region: residues 1614	to 1679
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The APC-rBC fragment interacts with two β-catenin molecules, indicating each 15aa repeat binds to one β-catenin molecule. In addition, APC-R2-R4 also interacts with two molecules of β-catenin, indicating that both APC-R3 and APC-R4, but not APC-R2, interact with one molecule of β-catenin simutaneously (Table 1). Thus our ITC study confirms the binding stoichiometry of one β-catenin binding repeat of APC to one β-catenin molecule.
This region corresponds to APC repeat 4 (APC-R4, residues 1614–1679).
Protein: DP00519 (UniProt P25054)
Region: residues 1202	to 1551
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
The two intrinsically disordered proteins (IDPs) AxinCR and β-caseine, however, were entirely digested at low TL concentration (0.001 g/L). Likewise, the band of APC-MCR disappeared at this TL concentration. We conclude that protease susceptibility of APC-MCR is similar to that of the IDPs Axin-CR and β-caseine.
Protein: DP00519 (UniProt P25054)
Region: residues 1202	to 1551
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In non-denaturing buffer and absence of TFE, we observed a minimum near 200 nm and absence of a negative peak at 220 nm indicating low α-helical structure content (Figure 3) [41].
Protein: DP00519 (UniProt P25054)
Region: residues 1202	to 1551
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We observed a linear decrease of fluorescence emission with increasing temperature, as it is typical for protein in the absence of global conformational changes (Figure 4A,B,C) [42]. We neither detected any thermally induced transition nor temperature-dependent changes in the spectral shape (Figure 4A, B). We conclude that temperature increase does not induce a structural transition that changes the environment of the intrinsic fluorescence probes in APC-MCR.
Protein: DP00519 (UniProt P25054)
Region: residues 1202	to 1551
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The elution time of APC-MCR corresponded to an apparent molecular weight of 200 kDa, 5-fold larger than expected based on its molecular weight of 40 kDa (Figure 5A,B). We conclude that APC-MCR is either predominantly extended or oligomeric.
The protein eluted as a single monomeric peak with a molecular mass of 44.4 ± 4.0 kDa. We conclude that APC-MCR is an extended intrinsically disordered region.
Protein: DP00519 (UniProt P25054)
Region: residues 1202	to 1551
Annotation: protein kinase binding (Molecular function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
In the presence of ATP and CK1ε, we incubated APC-MCR for up to 16 h and subsequently probed for an eventual change in migration pattern on SDS-PAGE. Additional negative charges locally prevent binding of SDS and, therefore, reduce mobility of the phosphorylated protein in the gel [21,44-47].
Our results demonstrate that APC-MCR can be phosphorylated by CK1ε.
Cross-references: ELM:MOD_CDK_SPxK_1
Protein: DP00519 (UniProt P25054)
Region: residues 1484	to 1528
Annotation: beta-catenin binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Unexpectedly, we were unable to detect binding of purified β-catenin arm repeat domain to GST-R7 immobilized on glutathione agarose beads, whereas robust binding was seen to GST-R3 (data not shown).
Protein: DP00519 (UniProt P25054)
Region: residues 1485	to 1498
Annotation: beta-catenin binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Both this triple Ser→Asp mutant, designated R3-tripleD, and the wild-type construct were used for cocrystallization trials with β-ARM.
Crystals were obtained only with the R3-tripleD (Table 1). Only 14 of the 47 residues of the APC construct are visible in the final electron density map. The final model consists of β-catenin residues 146-549 and 559-664, ICAT 8-53, and APC 1485-1498.
R3-tripleD corresponds to the APC peptide with the mutations S1501D, S1505D, and S1507D.
Cross-references: PDB:1T08
Protein: DP00519 (UniProt P25054)
Region: residues 1484	to 1528
Annotation: beta-catenin binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Isothermal titration calorimetry (ITC) measurements demonstrated that homogeneously phosphorylated R3 binds to full-length β-catenin with a dissociation constant KD of 10 ± 1.3 nM, as compared to the 3.1 ± 0.3 μM KD of the untreated material (Figures 3A and 3B
Protein: DP00519 (UniProt P25054)
Region: residues 1485	to 1499
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.
The structure of the pR3/β-catenin complex reveals that residues 1485 to 1499 bind to the arm repeat 5-9 groove identically to that observed in the unphosphorylated complex (Figure 3C).
Cross-references: PDB:1V18