LiteFold/DisProt huggingface dataset:
Protein: DP02376 (UniProt Q4ACU6)
Region: residues 377	to 532
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
This version of Shank3 contains known target binding domains/motifs and lacks most of the unstructured regions (Supplementary information, Fig. S3a, referred to as Shank3 from here on) as well as the previously identified active CaMKIIα binding site in the middle of the protein.
This contrasts with a recent finding that an unstructured fragment of Shank3 in the middle of the protein (aa 931–1014) binds to T286-autophosphorylated CaMKII.
The simplified version of Shank3 was generated by using an overlap PCR method to fuse multiple fragments, including residues 1–376 (NTD-ANK), 533–665 (N-PDZ), 1294–1323 (HBS), 1400–1426 (CBS) and 1654–1730 (SAM) with three point mutations (L231R, F304Y and M1718A) to improve solubility and homogeneity of the recombinant protein.
The authors consider the regions 377-532, 666-1295, 1324-1399 and 1427-1653 as unstructured.
Protein: DP02376 (UniProt Q4ACU6)
Region: residues 666	to 1293
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
This version of Shank3 contains known target binding domains/motifs and lacks most of the unstructured regions (Supplementary information, Fig. S3a, referred to as Shank3 from here on) as well as the previously identified active CaMKIIα binding site in the middle of the protein.
This contrasts with a recent finding that an unstructured fragment of Shank3 in the middle of the protein (aa 931–1014) binds to T286-autophosphorylated CaMKII.
The simplified version of Shank3 was generated by using an overlap PCR method to fuse multiple fragments, including residues 1–376 (NTD-ANK), 533–665 (N-PDZ), 1294–1323 (HBS), 1400–1426 (CBS) and 1654–1730 (SAM) with three point mutations (L231R, F304Y and M1718A) to improve solubility and homogeneity of the recombinant protein.
The authors consider the regions 377-532, 666-1293, 1324-1399 and 1427-1653 as unstructured.
Protein: DP02376 (UniProt Q4ACU6)
Region: residues 1324	to 1399
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
This version of Shank3 contains known target binding domains/motifs and lacks most of the unstructured regions (Supplementary information, Fig. S3a, referred to as Shank3 from here on) as well as the previously identified active CaMKIIα binding site in the middle of the protein.
This contrasts with a recent finding that an unstructured fragment of Shank3 in the middle of the protein (aa 931–1014) binds to T286-autophosphorylated CaMKII.
The simplified version of Shank3 was generated by using an overlap PCR method to fuse multiple fragments, including residues 1–376 (NTD-ANK), 533–665 (N-PDZ), 1294–1323 (HBS), 1400–1426 (CBS) and 1654–1730 (SAM) with three point mutations (L231R, F304Y and M1718A) to improve solubility and homogeneity of the recombinant protein.
The authors consider the regions 377-532, 666-1293, 1324-1399 and 1427-1653 as unstructured.
Protein: DP02376 (UniProt Q4ACU6)
Region: residues 1427	to 1653
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
This version of Shank3 contains known target binding domains/motifs and lacks most of the unstructured regions (Supplementary information, Fig. S3a, referred to as Shank3 from here on) as well as the previously identified active CaMKIIα binding site in the middle of the protein.
This contrasts with a recent finding that an unstructured fragment of Shank3 in the middle of the protein (aa 931–1014) binds to T286-autophosphorylated CaMKII.
The simplified version of Shank3 was generated by using an overlap PCR method to fuse multiple fragments, including residues 1–376 (NTD-ANK), 533–665 (N-PDZ), 1294–1323 (HBS), 1400–1426 (CBS) and 1654–1730 (SAM) with three point mutations (L231R, F304Y and M1718A) to improve solubility and homogeneity of the recombinant protein.
The authors consider the regions 377-532, 666-1293, 1324-1399 and 1427-1653 as unstructured.
Protein: DP02377 (UniProt Q9GRZ3)
Region: residues 1420	to 1441
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dashed lines represent regions of DPY−21 that are disordered and not built in the DPY−211210–1617 structure
Cross-references: PDB:5UQD
Protein: DP02377 (UniProt Q9GRZ3)
Region: residues 1458	to 1494
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dashed lines represent regions of DPY−21 that are disordered and not built in the DPY−211210–1617 structure
Cross-references: PDB:5UQD
Protein: DP02378 (UniProt Q09260)
Region: residues 115	to 132
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal domain of Sel-8 (Mastermind), residues 49–132, were cloned into pGEX-6P-1
The final refined model consists of CSL residues 195–267, 278–311, 319–372, 380–433, and 440–663, NotchIC residues 933–952 and 1021–1297, Mastermind residues 52–114
Cross-references: PDB:2FO1
Protein: DP02380 (UniProt O23661)
Region: residues 388	to 594
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
CD analysis of the ETT_388-594 construct showing characteristic spectrum of an unstructured protein
Circular dichroism and thermal stability analyses confirmed the bioinformatic predictions of near-complete disorder of the ES domain
Protein: DP02380 (UniProt O23661)
Region: residues 388	to 594
Annotation: molecular function activator activity (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
Analyses by Y2H revealed the ETT_388-594 construct retained full responsiveness to increases in auxin concentration (Fig. 4A; ETT-BD and ES-BD and ETT-388-594-BD rows) confirming it to be a stable and purifiable form of the ETT auxin-responsive domain capable of binding the Arabidopsis INDEHISCENT (IND) transcription factor used as the bait in the assay.
Protein: DP02380 (UniProt O23661)
Region: residues 388	to 594
Annotation: small molecule binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Analyses by Y2H revealed the ETT_388-594 construct retained full responsiveness to increases in auxin concentration (Fig. 4A; ETT-BD and ES-BD and ETT-388-594-BD rows) confirming it to be a stable and purifiable form of the ETT auxin-responsive domain capable of binding the Arabidopsis INDEHISCENT (IND) transcription factor used as the bait in the assay.
To probe the auxin sensing ability of the ES domain, random mutations were introduced into the ES domain sequence by error prone mutagenesis. A pool of ES mutants was cloned and tested in Y2H assay in the presence of IAA to isolate viable clones exhibiting IAA insensitivity. Tree ES domain variants were isolated (Fig.  4A, clones ES_EP1-3 BD) harbouring amino acid substitutions at the beginning (Fig.  4A, I393T, I424T, F445I) and the end (Fig.  4A, T562A, Y597H, D601G) of the ES domain. Mutations were also identified in proximity to the Motif 1B (Fig.  4A, Q436L) and in the Ser patch (Fig.  4A, S520T) which impair the auxin sensing property of the ETT-IND dimer. In parallel to the error-prone approach, we also introduced manually point mutations into the Ser patch by site-specific mutagenesis (S523T, S S524T, S526T and S527T; Fig.  4a). Interestingly, these specific mutations within the Ser patch strongly inhibited auxin perception.
Protein: DP02380 (UniProt O23661)
Region: residues 388	to 594
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
Analyses by Y2H revealed the ETT_388-594 construct retained full responsiveness to increases in auxin concentration (Fig. 4A; ETT-BD and ES-BD and ETT-388-594-BD rows) confirming it to be a stable and purifiable form of the ETT auxin-responsive domain capable of binding the Arabidopsis INDEHISCENT (IND) transcription factor used as the bait in the assay.
Protein: DP02381 (UniProt O60706-2)
Region: residues 618	to 669
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Two-dimensional 15N-HSQC spectra of the non-phosphorylated and phosphorylated L1
linker have limited dispersion in the 1H dimension, with almost all backbone amide 1H
resonances having chemical shifts of 7.9 to 8.6 ppm, and sharp resonances (Figure 1).
Resonances for L1 linker residues in spectra of L1-NBD1 also display limited dispersion and sharp line shapes (42). The limited dispersion of resonances in the 1H dimension is a
characteristic feature in the NMR spectra of disordered proteins and IDRs, in which each amide 1H nucleus experiences on average the same chemical environment.
Protein: DP02381 (UniProt O60706-2)
Region: residues 618	to 669
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Additionally, the L1 linker elutes from a size exclusion column at the volume expected for elution of globular proteins of ~14 kDa, rather than proteins of ~6 kDa that are the size of the L1 linker (Supplementary Figure 4). The earlier elution of the L1 linker is also consistent with its disordered nature and larger hydrodynamic radii of the ensemble of the L1 linker conformers compared to globular proteins of the same molecular weight
Protein: DP02381 (UniProt O60706-2)
Region: residues 618	to 669
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of the non-phosphorylated and phosphorylated L1 linker are typical of
what is observed for primarily disordered proteins
Protein: DP02381 (UniProt O60706-2)
Region: residues 618	to 669
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Phosphorylation of the L1 linker, by protein kinase A, disrupts its interactions with
NBD1, which increases the MgATP affinity of NBD1 and KATP channel gating.
Protein: DP02381 (UniProt O60706-2)
Region: residues 618	to 669
Annotation: molecular function regulator (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Phosphorylation of the L1 linker, by protein kinase A, disrupts its interactions with
NBD1, which increases the MgATP affinity of NBD1 and KATP channel gating.
Protein: DP02381 (UniProt O60706-2)
Region: residues 618	to 669
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Phosphorylation of the L1 linker, by protein kinase A, disrupts its interactions with the
NBD1 domain, which increases the MgATP affinity of NBD1 and KATP channel gating. 
Spectroscopic and biochemical studies indicate that the L1 linker possesses residual secondary and compact structure that is disrupted with phosphorylation, which leads to differential interactions of the nonphosphorylated and phosphorylated L1 linker with NBD1.
Protein: DP02382 (UniProt Q15046)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Interestingly, the apparent molecular weight (MW) of hRID in the gel was two-fold higher than the calculated MW (8.3 kDa). This phenomenon might result from the intrinsic disorder of the hRID structure
Protein: DP02382 (UniProt Q15046)
Region: residues 1	to 70
Annotation: disorder to order (Structural transition)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
Upon polyP addition, the circular dichroism (CD) score at 225 nm was decreased, and the CD score at 190 nm was increased, indicating that helical content increased.
Protein: DP02383 (UniProt P08631)
Region: residues 2	to 79
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The anticipated intrinsic disorder of these constructs (Amata et al. 2014) was evident in the low chemical shift dispersion in the 1H dimension (Fig.  1)
Cross-references: BMRB:27554
Protein: DP02383 (UniProt P08631)
Region: residues 2	to 79
Annotation: localization (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
the intrinsically disordered nature of the SH4 and Unique domains has resulted in a lack of information for this important region of the protein that is responsible for membrane association
These enzymes are often found anchored to the intracellular side of the membrane via lipidation of the SH4 domain and are integral components of signaling cascades localized at the cell surface.
Protein: DP02383 (UniProt P08631)
Region: residues 2	to 6
Annotation: myristoylation display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Both isoforms may be myristoylated at the N-terminus but p59Hck can also be palmitoylated on Cys3. The variable acylation is thought to be a major determinant in localizations within the cell: p59Hck is mainly associated with the plasma membrane and p61Hck with lysosomal membranes.
Protein: DP02383 (UniProt P08631)
Region: residues 2	to 21
Annotation: localization (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The two dominant isoforms of human Hck are referred to as p59Hck and p61Hck. The longer p61 isoform contains an additional 21 residues at the N-terminal end (MGGRSSCEDPGCPRDEERAPR), and is derived from an alternate start codon of the same mRNA. Both isoforms may be myristoylated at the N-terminus but p59Hck can also be palmitoylated on Cys3. The variable acylation is thought to be a major determinant in localizations within the cell: p59Hck is mainly associated with the plasma membrane and p61Hck with lysosomal membranes.
Protein: DP02383 (UniProt P08631)
Region: residues 2	to 79
Annotation: localization (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As in our previous work [39], we study an unmyristoylated construct of the Hck SH4-U domains containing residues 2–79, hereafter referred to as SH 4   UHck− (previously referred to as p61HckSH 4   U−). Experimental characterization of the average spatial distribution of SH 4   UHck− at the membrane surface is carried out using nuclear magnetic resonance (NMR) and neutron reflectometry (NR) experiments. Restrained-ensemble molecular dynamics (re-MD) simulations are then utilized to generate statistical models of membrane-bound Hck. The results confirm an interaction between the SH4 domain and acidic lipids, and yield an atomically detailed model of membrane bound SH 4   UHck−.
Protein: DP02383 (UniProt P08631)
Region: residues 2	to 79
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As in our previous work [39], we study an unmyristoylated construct of the Hck SH4-U domains containing residues 2–79, hereafter referred to as SH 4   UHck− (previously referred to as p61HckSH 4   U−). Experimental characterization of the average spatial distribution of SH 4   UHck− at the membrane surface is carried out using nuclear magnetic resonance (NMR) and neutron reflectometry (NR) experiments. Restrained-ensemble molecular dynamics (re-MD) simulations are then utilized to generate statistical models of membrane-bound Hck. The results confirm an interaction between the SH4 domain and acidic lipids, and yield an atomically detailed model of membrane bound SH 4   UHck−.
Protein: DP02384 (UniProt P82804)
Region: residues 33	to 58
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the crystallized construct contains 25 additional C-terminal residues, these are disordered in the structure and do not contribute to Mago–Y14 binding
Cross-references: PDB:1RK8
Protein: DP02386 (UniProt Q9NYB9)
Region: residues 156	to 513
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We next sought to determine where and how the WIRS motif binds to the WRC. For this, we determined the 2.43-Å crystal structure of a complex cocrystallized from a variant of the WIRS-containing peptide (WGAERSM∗STFGKEKA, M∗ for selenomethionine, Figure 1B) and a minimal inhibited WRC, which lacks the C terminus of Abi and the proline-rich region of WAVE, miniWRC (Figure 2 and Table S1) (Chen et al., 2010).
Cross-references: PDB:4N78
Protein: DP02387 (UniProt P70429)
Region: residues 114	to 130
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of density corresponding to the N- and C-terminal residues of the peptides is consistent with deletion studies showing no significant effect on binding unless residues within the FPPPP core are deleted
Cross-references: PDB:1QC6
Protein: DP02389 (UniProt Q96GD4)
Region: residues 221	to 236
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the Aurora B:INCENP complex, the activation segment is disordered after the DFG motif, including the phosphorylation site Thr232. The C-terminal part of the activation segment is dislodged from the lower lobe and interacts with a deep groove generated by the displaced activation segment in the interacting protomer. Overall, there is a buried surface area of interaction of 3460 Å2, and the segment is anchored mainly by aromatic and hydrophobic interactions of Y239, L237, Pro242, and I245
Cross-references: PDB:4AF3
Protein: DP02389 (UniProt Q96GD4)
Region: residues 230	to 234
Annotation: phosphorylation display site (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the Aurora B:INCENP complex, the activation segment is disordered after the DFG motif, including the phosphorylation site Thr232. 
Cross-references: PDB:4AF3
Protein: DP02389 (UniProt Q96GD4)
Region: residues 230	to 234
Annotation: phosphorylation display site (Disorder function)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
We report here evidence that human Aurora-B is phosphorylated at Thr-232 through interaction with the INCENP in vivo. This phosphorylation of Thr-232 occurs by means of an autophosphorylation mechanism and is essential for the Aurora-B kinase activity.
Protein: DP02389 (UniProt Q96GD4)
Region: residues 221	to 236
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the Aurora B:INCENP complex, the activation segment is disordered after the DFG motif, including the phosphorylation site Thr232. The C-terminal part of the activation segment is dislodged from the lower lobe and interacts with a deep groove generated by the displaced activation segment in the interacting protomer. Overall, there is a buried surface area of interaction of 3460 Å2, and the segment is anchored mainly by aromatic and hydrophobic interactions of Y239, L237, Pro242, and I245
we determined the structure of human Aurora B kinase domain, in complex with the C-terminal IN-box section of human INCENP (residues 835–903)
Cross-references: PDB:4AF3
Protein: DP02389 (UniProt Q96GD4)
Region: residues 221	to 236
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We report here evidence that human Aurora-B is phosphorylated at Thr-232 through interaction with the INCENP in vivo. This phosphorylation of Thr-232 occurs by means of an autophosphorylation mechanism and is essential for the Aurora-B kinase activity.
Protein: DP02390 (UniProt Q9NQS7)
Region: residues 883	to 903
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Therefore, a bacterial expression construct for the C-terminal part of human INCENP was prepared, spanning residues 835–903, which is the Aurora-binding region.
To provide a model for structure-based design and to gain insight into the molecular mechanism of human Aurora B activation, we determined the structure of human Aurora B kinase domain, in complex with the C-terminal IN-box section of human INCENP (residues 835–903) and the type II inhibitor 1 (Figure ​(Figure11).
Cross-references: PDB:4AF3
Protein: DP02390 (UniProt Q9NQS7)
Region: residues 853	to 903
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Therefore, a bacterial expression construct for the C-terminal part of human INCENP was prepared, spanning residues 835–903, which is the Aurora-binding region.
To provide a model for structure-based design and to gain insight into the molecular mechanism of human Aurora B activation, we determined the structure of human Aurora B kinase domain, in complex with the C-terminal IN-box section of human INCENP (residues 835–903) and the type II inhibitor 1 (Figure ​(Figure11).
Cross-references: PDB:4AF3
Protein: DP02390 (UniProt Q9NQS7)
Region: residues 892	to 896
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We next evaluated whether or not the TSS motif (T893, S894, S895) within the IN box domain of INCENP is involved in Aurora-C activation
In vitro kinase assays on pulled down protein complexes from Sf-9 cells co-infected with WT or 3A mutant of INCENP together with the Aurora-B and -C kinases also confirmed the role of the TSS motif phosphorylation of INCENP in the activation of the two kinases
Protein: DP02390 (UniProt Q9NQS7)
Region: residues 883	to 903
Annotation: molecular function activator activity (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
We next evaluated whether or not the TSS motif (T893, S894, S895) within the IN box domain of INCENP is involved in Aurora-C activation
In vitro kinase assays on pulled down protein complexes from Sf-9 cells co-infected with WT or 3A mutant of INCENP together with the Aurora-B and -C kinases also confirmed the role of the TSS motif phosphorylation of INCENP in the activation of the two kinases
Protein: DP02392 (UniProt Q9ZVD0)
Region: residues 290	to 324
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The presence of three disordered loops (residues 290–324, 366–380 and 435–444) in Middle domain implicates its role in protein–protein interaction with SE partners and/or substrates.
SE might possess structural features to sort out the substrates among RNAs rich in variety of size and structures, and to allocate binding partners to form either splicing or dicing complexes
Cross-references: PDB:3AX1