LiteFold/DisProt huggingface dataset:
Protein: DP01136 (UniProt P22470)
Region: residues 1	to 610
Annotation: ubiquitin-protein transferase activity (Molecular function)
Evidence: in vivo ubiquitination assay evidence used in manual assertion
Supporting statements:
We also examined San1-dependent ubiquitination of select GAD-fusion substrates using the in coli assay and found they were ubiquitinated in a San1-dependent manner (Figure 5D), indicating San1 directly targets these substrates as well.
Protein: DP01136 (UniProt P22470)
Region: residues 1	to 610
Annotation: positive regulation of proteolysis involved in cellular protein catabolic process (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We analyzed the degradation of each GAD fusion and found 25 of 28 required San1 to be fully degraded: 14 underwent primarily San1-dependent degradation (Figures 5A and S4A), 11 were subject to degradation that was partially dependent on San1 (Figures 5B and S4A), and 3 were stable when San1 was present (Figure 5C).
Protein: DP01137 (UniProt Q6FI81)
Region: residues 173	to 266
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectra of the full-length protein shows highly crowded cross-peaks in the spectral region between 8 and 8.5 ppm indicating that the protein contains an unstructured region, in addition to several signals spread over a larger spectral range, indicative of folded conformations. After degradation, the 1H-15N HSQC spectrum of the resulting fragment shows the disappearance of many of the signals in the crowded, central region, whereas the well-resolved resonances are still present and do not show significant chemical shift changes. 15N{1H} NOEs experiments on the full-length anamorsin showed that the residues not belonging to the N-terminal domain (that are all in the highly crowded spectral region between 8 and 8.5 ppm) exhibited negative or very low NOEs, indicative of a high degree of flexibility in the C-terminal part of the protein. We can conclude that the N-terminal part is well-folded whereas the C-terminal part, comprising both the linker and CIAPIN1 domain, is largely unstructured and flexible and therefore, highly prone to degradation.
Protein: DP01137 (UniProt Q6FI81)
Region: residues 173	to 266
Annotation: iron ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Anamorsin contains a well-folded N-terminal domain and a largely unstructured, flexible C-terminal part, containing a CIAPIN1 domain with highly conserved cysteine pattern. Secondary structure and folding predictions reveal that these two domains in anamorsin are separated by an unstructured amino acid linker of ∼50 residues and that a large part of the CIAPIN1 domain, in particular its initial segment (residues 222–266), is structurally highly disordered, whereas the final segment is predicted to be more structured. The latter region of the CIAPIN1 domain contains a twin CX2C motif whereas the initial segment of the CIAPIN1 domain contains the four additional cysteines of the highly conserved cysteine pattern. It is likely that cysteines of the highly conserved cysteine pattern in anamorsin are involved in iron binding. Mass spectrometry analysis revealed that the stable fragment is constituted by the N-terminal part spanning aa 1–172 of the protein. During degradation, the color of the anamorsin solution is lost, indicating that iron is released. Because the remaining stable fragment does not contain cysteines of the CIAPIN1 domain, at least one of the latter cysteines is essential for iron binding.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 129	to 160
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of RPELs exhibited a strong negative band near 200 nm and a weak negative shoulder at 220 nm, which is characteristic of unfolded polypeptides. This is supported by the prediction of structural disorder by IUPred, which indicates that RPEL1(85-116), RPEL2(129-160), and RPEL3 (173-204) are disordered. The negative band near 200 nm is stronger in the order of RPEL3 > RPEL2 > RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 129	to 160
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Mouilleron et al. have shown that RPEL1 and RPEL2 bind to G-actin tightly, with dissociation constants (Kd) of 1.0 and 1.9 μM, respectively. They also showed that RPEL3 binds weakly to G-actin with a Kd value of 28.9 μM, although the essential residues for the interaction with G-actin are conserved in RPEL3. From these Kd values, the Gibbs free energy changes (ΔG0) of binding are −8.2 kcal/mol, −7.8 kcal/mol, and −6.2 kcal/mol for RPEL1, RPEL2, and RPEL3, respectively. The helical propensity is higher in the order of RPEL1, RPEL2, and RPEL3. These results suggest that the amount of preformed structure may correlate with the ΔG0 value of binding. It is conceivable that the binding strength between IDP and the target molecule is modulated by the preformed structural elements in free IDP.
Cross-references: PMID:19008859
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 129	to 160
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
According to the crystal structures of RPEL1 and RPEL2 in complex with G-actin, the RPEL motif adopts two α-helices and binds to the hydrophobic cleft and the hydrophobic ledge of G-actin. The essential residues for actin binding are completely conserved between RPEL2 and RPEL3, while the essential residues are partially different between RPEL1 and RPEL2: Ile140 and Leu155 of RPEL2 are substituted with Leu and Met in RPEL1, although Leu136, Lys139, Arg143, Leu149, and Ile154 of RPEL2 are conserved in RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 129	to 160
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
According to the crystal structures of RPEL1 and RPEL2 in complex with G-actin, the RPEL motif adopts two α-helices and binds to the hydrophobic cleft and the hydrophobic ledge of G-actin. The essential residues for actin binding are completely conserved between RPEL2 and RPEL3, while the essential residues are partially different between RPEL1 and RPEL2: Ile140 and Leu155 of RPEL2 are substituted with Leu and Met in RPEL1, although Leu136, Lys139, Arg143, Leu149, and Ile154 of RPEL2 are conserved in RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 129	to 160
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Mouilleron et al. have shown that RPEL1 and RPEL2 bind to G-actin tightly, with dissociation constants (Kd) of 1.0 and 1.9 μM, respectively. They also showed that RPEL3 binds weakly to G-actin with a Kd value of 28.9 μM, although the essential residues for the interaction with G-actin are conserved in RPEL3. From these Kd values, the Gibbs free energy changes (ΔG0) of binding are −8.2 kcal/mol, −7.8 kcal/mol, and −6.2 kcal/mol for RPEL1, RPEL2, and RPEL3, respectively. The helical propensity is higher in the order of RPEL1, RPEL2, and RPEL3. These results suggest that the amount of preformed structure may correlate with the ΔG0 value of binding. It is conceivable that the binding strength between IDP and the target molecule is modulated by the preformed structural elements in free IDP.
Cross-references: PMID:19008859
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 173	to 204
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of RPELs exhibited a strong negative band near 200 nm and a weak negative shoulder at 220 nm, which is characteristic of unfolded polypeptides. This is supported by the prediction of structural disorder by IUPred, which indicates that RPEL1(85-116), RPEL2(129-160), and RPEL3 (173-204) are disordered. The negative band near 200 nm is stronger in the order of RPEL3 > RPEL2 > RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 173	to 204
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Mouilleron et al. have shown that RPEL1 and RPEL2 bind to G-actin tightly, with dissociation constants (Kd) of 1.0 and 1.9 μM, respectively. They also showed that RPEL3 binds weakly to G-actin with a Kd value of 28.9 μM, although the essential residues for the interaction with G-actin are conserved in RPEL3. From these Kd values, the Gibbs free energy changes (ΔG0) of binding are −8.2 kcal/mol, −7.8 kcal/mol, and −6.2 kcal/mol for RPEL1, RPEL2, and RPEL3, respectively. The helical propensity is higher in the order of RPEL1, RPEL2, and RPEL3. These results suggest that the amount of preformed structure may correlate with the ΔG0 value of binding. It is conceivable that the binding strength between IDP and the target molecule is modulated by the preformed structural elements in free IDP.
Cross-references: PMID:19008859
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 173	to 204
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
According to the crystal structures of RPEL1 and RPEL2 in complex with G-actin, the RPEL motif adopts two α-helices and binds to the hydrophobic cleft and the hydrophobic ledge of G-actin. The essential residues for actin binding are completely conserved between RPEL2 and RPEL3, while the essential residues are partially different between RPEL1 and RPEL2: Ile140 and Leu155 of RPEL2 are substituted with Leu and Met in RPEL1, although Leu136, Lys139, Arg143, Leu149, and Ile154 of RPEL2 are conserved in RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 173	to 204
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
According to the crystal structures of RPEL1 and RPEL2 in complex with G-actin, the RPEL motif adopts two α-helices and binds to the hydrophobic cleft and the hydrophobic ledge of G-actin. The essential residues for actin binding are completely conserved between RPEL2 and RPEL3, while the essential residues are partially different between RPEL1 and RPEL2: Ile140 and Leu155 of RPEL2 are substituted with Leu and Met in RPEL1, although Leu136, Lys139, Arg143, Leu149, and Ile154 of RPEL2 are conserved in RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 173	to 204
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Mouilleron et al. have shown that RPEL1 and RPEL2 bind to G-actin tightly, with dissociation constants (Kd) of 1.0 and 1.9 μM, respectively. They also showed that RPEL3 binds weakly to G-actin with a Kd value of 28.9 μM, although the essential residues for the interaction with G-actin are conserved in RPEL3. From these Kd values, the Gibbs free energy changes (ΔG0) of binding are −8.2 kcal/mol, −7.8 kcal/mol, and −6.2 kcal/mol for RPEL1, RPEL2, and RPEL3, respectively. The helical propensity is higher in the order of RPEL1, RPEL2, and RPEL3. These results suggest that the amount of preformed structure may correlate with the ΔG0 value of binding. It is conceivable that the binding strength between IDP and the target molecule is modulated by the preformed structural elements in free IDP.
Cross-references: PMID:19008859
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 85	to 116
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum of RPEL1 (85-116) shows the backbone amide resonances within 8.0–8.6 ppm in the 1H dimension. The narrow chemical shift dispersion in the 1H dimension is characteristic of intrinsically disordered proteins (IDPs).
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 85	to 116
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
According to the crystal structures of RPEL1 and RPEL2 in complex with G-actin, the RPEL motif adopts two α-helices and binds to the hydrophobic cleft and the hydrophobic ledge of G-actin. The essential residues for actin binding are completely conserved between RPEL2 and RPEL3, while the essential residues are partially different between RPEL1 and RPEL2: Ile140 and Leu155 of RPEL2 are substituted with Leu and Met in RPEL1, although Leu136, Lys139, Arg143, Leu149, and Ile154 of RPEL2 are conserved in RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 85	to 116
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Mouilleron et al. have shown that RPEL1 and RPEL2 bind to G-actin tightly, with dissociation constants (Kd) of 1.0 and 1.9 μM, respectively. They also showed that RPEL3 binds weakly to G-actin with a Kd value of 28.9 μM, although the essential residues for the interaction with G-actin are conserved in RPEL3. From these Kd values, the Gibbs free energy changes (ΔG0) of binding are −8.2 kcal/mol, −7.8 kcal/mol, and −6.2 kcal/mol for RPEL1, RPEL2, and RPEL3, respectively. The helical propensity is higher in the order of RPEL1, RPEL2, and RPEL3. These results suggest that the amount of preformed structure may correlate with the ΔG0 value of binding. It is conceivable that the binding strength between IDP and the target molecule is modulated by the preformed structural elements in free IDP.
Cross-references: PMID:19008859
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 85	to 116
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of RPELs exhibited a strong negative band near 200 nm and a weak negative shoulder at 220 nm, which is characteristic of unfolded polypeptides. This is supported by the prediction of structural disorder by IUPred, which indicates that RPEL1(85-116), RPEL2(129-160), and RPEL3 (173-204) are disordered. The negative band near 200 nm is stronger in the order of RPEL3 > RPEL2 > RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 85	to 116
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
According to the crystal structures of RPEL1 and RPEL2 in complex with G-actin, the RPEL motif adopts two α-helices and binds to the hydrophobic cleft and the hydrophobic ledge of G-actin. The essential residues for actin binding are completely conserved between RPEL2 and RPEL3, while the essential residues are partially different between RPEL1 and RPEL2: Ile140 and Leu155 of RPEL2 are substituted with Leu and Met in RPEL1, although Leu136, Lys139, Arg143, Leu149, and Ile154 of RPEL2 are conserved in RPEL1.
Protein: DP01139 (UniProt A0A0G2JXC5)
Region: residues 85	to 116
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Mouilleron et al. have shown that RPEL1 and RPEL2 bind to G-actin tightly, with dissociation constants (Kd) of 1.0 and 1.9 μM, respectively. They also showed that RPEL3 binds weakly to G-actin with a Kd value of 28.9 μM, although the essential residues for the interaction with G-actin are conserved in RPEL3. From these Kd values, the Gibbs free energy changes (ΔG0) of binding are −8.2 kcal/mol, −7.8 kcal/mol, and −6.2 kcal/mol for RPEL1, RPEL2, and RPEL3, respectively. The helical propensity is higher in the order of RPEL1, RPEL2, and RPEL3. These results suggest that the amount of preformed structure may correlate with the ΔG0 value of binding. It is conceivable that the binding strength between IDP and the target molecule is modulated by the preformed structural elements in free IDP.
Cross-references: PMID:19008859
Protein: DP01140 (UniProt P38293)
Region: residues 1	to 148
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The logarithmic plot of these calculated Rs values versus the molecular masses of the corresponding monomeric and dimeric Ump1 variants indicates that these proteins do not behave as natively folded globular proteins in solution, and fall very close to the plot representing the behaviour of molecules with a natively unfolded molten globule conformation
Protein: DP01140 (UniProt P38293)
Region: residues 1	to 148
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra for all proteins (monomeric and dimeric wild-type Ump1, as well as Ump1-C115S mutant) exhibit isodichroic curves, with a minimum at 201 nm and a shoulder around 222 nm.
Protein: DP01140 (UniProt P38293)
Region: residues 1	to 148
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
all preparations of wild-type Ump1 exhibit a very gradual – and almost constant – CD signal variation with temperature, from 25 to 90°C. This is unlike the typical behaviour of small, single domain folded globular proteins, where the unfolding is highly cooperative and occurs in a very narrow temperature range. Also, even at 90°C, Ump1 does not seem to be fully denatured...
Protein: DP01140 (UniProt P38293)
Region: residues 1	to 84
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra from this Ump1 N-terminal proteolytic fragment confirm that, in accordance with the theoretical disorder predictions (Figure 2 and S2), the N-terminal region is largely unstructured (Figure 5).
Protein: DP01140 (UniProt P38293)
Region: residues 1	to 148
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Backbone chemical shift data indicated that Ump1 is an intrinsically unstructured protein and largely devoid of secondary structural elements.
Figure 1 shows the 1H–15N HSQC spectrum of Ump1 recorded at 30 °C. The HSQC peaks were observed within a narrow spectral region (7.3–8.5 ppm for the 1H chemical shifts), which indicated that Ump1 was largely unstructured in solution.
Protein: DP01141 (UniProt P70604)
Region: residues 396	to 424
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Positive NOE values indicative for increased rigidity were observed for residues between Ala-425 and Tyr-435, while negative values were obtained outside this region. Together, the NOE pattern and the results from dynamic measurements suggested that CaMBD consists of an ordered most likely helical core region flanked by flexible N and C termini.
Cross-references: PDB:1KKD
Protein: DP01141 (UniProt P70604)
Region: residues 396	to 424
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Both types of interactions with CaM require a domain of about 90 amino acids in the proximal C terminus of the channel subunit, the calmodulin binding domain (CaMBD). As long as the CaMBD is present at the C terminus of the SK α-subunit, channels exhibit regular Ca2+-gating; deletions of more than 10 residues resulted in channels that were no longer gated by intracellular Ca2+.
Protein: DP01141 (UniProt P70604)
Region: residues 436	to 487
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Positive NOE values indicative for increased rigidity were observed for residues between Ala-30 and Tyr-40, while negative values were obtained outside this region. Together, the NOE pattern and the results from dynamic measurements suggested that CaMBD consists of an ordered most likely helical core region flanked by flexible N and C termini.
Cross-references: PDB:1KKD
Protein: DP01141 (UniProt P70604)
Region: residues 436	to 487
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Both types of interactions with CaM require a domain of about 90 amino acids in the proximal C terminus of the channel subunit, the calmodulin binding domain (CaMBD). As long as the CaMBD is present at the C terminus of the SK α-subunit, channels exhibit regular Ca2+-gating; deletions of more than 10 residues resulted in channels that were no longer gated by intracellular Ca2+.
Protein: DP01142 (UniProt O92972)
Region: residues 2314	to 2338
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Adding a small amount of Bin1–SH3 (molar ratio of 5:1) only affects the line widths and chemical shifts of amide resonances in the region 342 to 366 (Fig. 4a) comprising three canonical SH3 binding sites (PPII helix motifs): one of class I [PP1.2 (348–354)] and two of class II [PP2.1 (343–348) and PP2.2 (351–356)] (Fig. 4c).
Residues 342-366 of the nonstructural protein 5A (NS5A) from Hepatitis C virus genotype 1b (strain HC-J4) corresponds to 2314-2338 residues of the polyprotein.
Protein: DP01142 (UniProt O92972)
Region: residues 2163	to 2341
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Kratky representation of these data, shown in Fig. 3d, is characteristic of a highly disordered protein. Nevertheless, a small bump observed in this scattering curve (at s ≈ 0.7) is indicative of a certain degree of compactness.
For most residues, the absolute values of these secondary chemical shifts are below 1.0 to 1.5 ppm, indicating the absence of any persistent secondary structure in this protein fragment consistent with an IDP.
Protein: DP01142 (UniProt O92972)
Region: residues 2305	to 2341
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
This refers to a macroscopic system with a high binding affinity of the two proteins, consistent with a Kd of 0.1 μM measured by surface plasmon resonance for a short NS5A(333–369) fragment that comprises the entire poly-proline rich region (Fig. S6).
Residues 333-369 of the nonstructural protein 5A (NS5A) from Hepatitis C virus genotype 1b (strain HC-J4) corresponds to 2305-2341 residues of the polyprotein.
Protein: DP01142 (UniProt O92972)
Region: residues 2172	to 2200
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon addition of SH3 at concentrations higher than the equimolar concentration, chemical shift changes were observed for NS5A residues 200–228 (binding site B1) and 295–320 (binding site B2).
Residues 200-228 (B1) of the nonstructural protein 5A (NS5A) from Hepatitis C virus genotype 1b (strain HC-J4) corresponds to 2172-2200 residues of the polyprotein.