LiteFold/DisProt huggingface dataset:
Protein: DP03136 (UniProt F4IED2)
Region: residues 200	to 230
Annotation: self-assembly (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ANAC013 IDR interacts with the DBD through negatively charged islands—AIs
The two other regions with increased R2values were S200–Q230, AD1/AI2, comprising the transient helix, and V240–E270, AD2/AI3, comprising the RIM (Fig. ​(Fig.1A).1A).
 We therefore hypothesized that the IDR interacts with the DBD through dynamic electrostatic interactions between negatively (IDR) and positively (DBD) charged areas. Indeed, R2 rates showed a gradual decrease across the IDR with increasing ionic strength (Fig. ​(Fig.1E, middle1E, middle panel), reflecting screening of the DBD–IDR interaction involving the AD1/AI2 and AD2/AI3 and confirming the observed interactions to be mainly electrostatic.
Protein: DP03136 (UniProt F4IED2)
Region: residues 240	to 270
Annotation: self-assembly (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ANAC013 IDR interacts with the DBD through negatively charged islands—AIs
The two other regions with increased R2values were S200–Q230, AD1/AI2, comprising the transient helix, and V240–E270, AD2/AI3, comprising the RIM (Fig. ​(Fig.1A).1A).
 We therefore hypothesized that the IDR interacts with the DBD through dynamic electrostatic interactions between negatively (IDR) and positively (DBD) charged areas. Indeed, R2 rates showed a gradual decrease across the IDR with increasing ionic strength (Fig. ​(Fig.1E, middle1E, middle panel), reflecting screening of the DBD–IDR interaction involving the AD1/AI2 and AD2/AI3 and confirming the observed interactions to be mainly electrostatic.
Protein: DP03136 (UniProt F4IED2)
Region: residues 254	to 274
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To decompose a possible second RCD1-RST binding site in ANAC013, we first re-established the interaction between the ANAC013-RIM (N254–T274) and RCD1-RST using ITC at the current conditions, showing the formation of a 1:1 complex with a KD of 70 ± 30 nM (Table 2 and Fig. 3A, left panel) consistent with previous work (KD = 9 ± 4 nM; different buffers [21]).
Protein: DP03136 (UniProt F4IED2)
Region: residues 254	to 274
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
ANAC013 resonances did not show measurable CSPs upon RCD1-RST addition but underwent extensive line broadening, suggesting slow exchange on the NMR timescale (Fig. 3B and Supplementary Fig. S10A). In both instances, residues corresponding to the RIM (N254–T274) located in AD2/AI3 were broadened beyond detection at a 1:1 ratio of RCD1-RST:ANAC013 (Fig. 3B and Supplementary Fig. S10B).
Cross-references: BMRB:51970
Protein: DP03136 (UniProt F4IED2)
Region: residues 220	to 230
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, a second interaction site was identified in ANAC013 between I220 and Q230, corresponding to the transient helix located in AD1/AI2 (Fig. 1E and Supplementary Fig. S2). For this second site, which bears sequence similarities to the known RIM (Supplementary Fig. S10C), resonances were broadened beyond detection at a ratio of RCD1-RST:ANAC013161–274 of 1.5:1, suggesting a weaker affinity compared to RIM1 (Fig. 4B). We term this second site RIM2 (residues I220–Q230), keeping the known site (N254–T274) as RIM1 (Fig. 1A).
Cross-references: BMRB:51970
Protein: DP03136 (UniProt F4IED2)
Region: residues 204	to 234
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To investigate the RIM2 interaction with RCD1-RST separately, we produced ANAC013204–234 and studied the interaction by ITC. This revealed a KD of 11 ± 2 μM (Table 2 and Fig. 3A, middle panel). The large entropic penalty (–TΔS = 25 ± 5 kJ mol−1) as well as large enthalpy contribution (ΔH = −53 ± 5 kJ mol−1) suggested that the transient helix (D217–G232) would fold further upon binding.
Protein: DP03136 (UniProt F4IED2)
Region: residues 217	to 232
Annotation: disorder to order (Structural transition)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
To investigate the RIM2 interaction with RCD1-RST separately, we produced ANAC013204–234 and studied the interaction by ITC. This revealed a KD of 11 ± 2 μM (Table 2 and Fig. 3A, middle panel). The large entropic penalty (–TΔS = 25 ± 5 kJ mol−1) as well as large enthalpy contribution (ΔH = −53 ± 5 kJ mol−1) suggested that the transient helix (D217–G232) would fold further upon binding.
Protein: DP03137 (UniProt Q9LUA9)
Region: residues 175	to 208
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Experimental analysis for secondary structure content by far-UV CD indicated low α-helical contents of 12, 18, 10, and 13% in the ANAC013(254–274), DREB2A(255–272), COL10(175–208), and bZIP23(15–36) peptides, respectively (Fig. 5, B–E).
Protein: DP03137 (UniProt Q9LUA9)
Region: residues 175	to 208
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Putative RCD1-binding motifs were also identified for the B-box transcription factors STO and COL10 (Fig. 3A), which bound RCD1 both in vivo and in vitro (14). Here, the Kd values for the interactions of RCD1 with the STO and COL10 peptides were determined to 90 and 418 nm, respectively. Interestingly, in both cases the change in binding enthalpy was low, −3.8 kJ/mol and −9.2 kJ/mol, respectively, which could be explained by entropy-driven interactions (Table 2).
Protein: DP03138 (UniProt Q8GTS2)
Region: residues 15	to 36
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Experimental analysis for secondary structure content by far-UV CD indicated low α-helical contents of 12, 18, 10, and 13% in the ANAC013(254–274), DREB2A(255–272), COL10(175–208), and bZIP23(15–36) peptides, respectively (Fig. 5, B–E).
Protein: DP03138 (UniProt Q8GTS2)
Region: residues 15	to 36
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Peptide bZIP23(15–36), derived from bZIP23, a member of the basic ZIP transcription factor family, interacted with RCD1 with an affinity corresponding to a Kd of 128 nm, comparable with that of the DREB2A·RCD1 interaction (Table 2).
Protein: DP03139 (UniProt Q4VP08)
Region: residues 20	to 52
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal segment (residues 20–52) of AtLURE1.2 is completely disordered, whereas its C-terminal portion (residues 53–89) adopts a typical structure of plant defensin peptides characterized by cysteine-stabilized αβ-motif (CSαβ)
Therefore, whether and how the N-terminal (residues 21–52) disordered in our structure contributes to AtLURE1.2-induced signaling remain unknown.
Cross-references: PDB:5Y9W
PDB:5YAH
Protein: DP03140 (UniProt O50008)
Region: residues 448	to 460
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The model was extended to a total of 746 residues (residues 1 and 418–460 were not observed in the electronic density) by manual building using the O molecular modeling package.
Residues 448-460 are missing from the PDBs structures
Cross-references: PDB:1U1J
PDB:1U1H
PDB:1U1U
PDB:1U22
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 226	to 269
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the 1H-15N HSQC spectrum of the free 13C,15N-hNIFK226–2693P peptide (Fig. 1, black contours), the amide resonances of the phosphorylated residues, pSer230, pThr234 and pThr238, were all substantially downfield shifted, consistent with known shift effects of phosphorylation. However, the small spectral dispersion of all other backbone 1HN resonances (7.9–8.5 p.p.m.) clearly indicated that the peptide is essentially unstructured.
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 226	to 269
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon interaction with Ki67FHA (Fig. 1, red), all resonances showed substantially increased chemical shift dispersion (7.0–10.2 p.p.m.), indicating that the random-coiled peptide adopts a well-defined structure.
For hNIFK226–2693P, on the other hand, a substantial conformational change between the free and bound structures occurs: residues 239–251 become α-helical and residues 260–264 adopt a β-strand conformation. Most notably, this β-strand extends the β-sheet of Ki67FHA, running antiparallel to β4. Residues residing on the α-helix interact with the β4-β5 and β10-β11 loops of Ki67FHA. The peptide shows close packing against Ki67FHA and buries a large surface area of Ki67FHA (1,450 Å2 of a total 6,037 Å2).
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 226	to 269
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon interaction with Ki67FHA (Fig. 1, red), all resonances showed substantially increased chemical shift dispersion (7.0–10.2 p.p.m.), indicating that the random-coiled peptide adopts a well-defined structure.
For hNIFK226–2693P, on the other hand, a substantial conformational change between the free and bound structures occurs: residues 239–251 become α-helical and residues 260–264 adopt a β-strand conformation. Most notably, this β-strand extends the β-sheet of Ki67FHA, running antiparallel to β4. Residues residing on the α-helix interact with the β4-β5 and β10-β11 loops of Ki67FHA. The peptide shows close packing against Ki67FHA and buries a large surface area of Ki67FHA (1,450 Å2 of a total 6,037 Å2).
Cross-references: PDB:2AFF
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 226	to 269
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Dissociation constants (Kd) for the Ki67FHA–hNIFK226–269 complexes were determined using surface plasmon resonance (SPR) (Table 1). hNIFK226–2693P bound tightly to Ki67FHA, with a Kd value of 0.077 μM, and the doubly phosphorylated S230A mutant showed only slightly weaker binding.
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 228	to 232
Annotation: phosphorylation display site (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The forkhead-associated (FHA) domain of human Ki67 interacts with the human nucleolar protein hNIFK, recognizing a 44-residue fragment, hNIFK226–269, phosphorylated at Thr234. Here we show that high-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230.
We speculated that Ser230 might be the third residue and confirmed this proposal by mutagenesis. Phosphorylation of hNIFK226–269 S230A by both kinases resulted only in double phosphorylation (Supplementary Table 1 online).
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 232	to 236
Annotation: phosphorylation display site (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The forkhead-associated (FHA) domain of human Ki67 interacts with the human nucleolar protein hNIFK, recognizing a 44-residue fragment, hNIFK226–269, phosphorylated at Thr234. Here we show that high-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230.
Given that GSK3 can uniquely recognize a priming phosphoryl group at +4 serine or threonine, we tested for the possibility that phosphorylation of Thr234 by GSK3 proceeds only after Thr238 is already phosphorylated by CDK1. Such double phosphorylation was indeed observed and confirmed by MS and mutagenesis. Only a single residue, Thr238, became phosphorylated in the T234A mutant of hNIFK226–269 when both kinases were used.
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 232	to 236
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
The forkhead-associated (FHA) domain of human Ki67 interacts with the human nucleolar protein hNIFK, recognizing a 44-residue fragment, hNIFK226–269, phosphorylated at Thr234. Here we show that high-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230.
Given that GSK3 can uniquely recognize a priming phosphoryl group at +4 serine or threonine, we tested for the possibility that phosphorylation of Thr234 by GSK3 proceeds only after Thr238 is already phosphorylated by CDK1. Such double phosphorylation was indeed observed and confirmed by MS and mutagenesis. Only a single residue, Thr238, became phosphorylated in the T234A mutant of hNIFK226–269 when both kinases were used.
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 236	to 240
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
The forkhead-associated (FHA) domain of human Ki67 interacts with the human nucleolar protein hNIFK, recognizing a 44-residue fragment, hNIFK226–269, phosphorylated at Thr234. Here we show that high-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230.
Mass spectrometry (MS) analyses indicated a single phosphorylation, and the amino acid target of phosphorylation was identified as Thr238 by mutagenesis.
Protein: DP03141 (UniProt Q9BYG3)
Region: residues 236	to 240
Annotation: phosphorylation display site (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The forkhead-associated (FHA) domain of human Ki67 interacts with the human nucleolar protein hNIFK, recognizing a 44-residue fragment, hNIFK226–269, phosphorylated at Thr234. Here we show that high-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230.
Mass spectrometry (MS) analyses indicated a single phosphorylation, and the amino acid target of phosphorylation was identified as Thr238 by mutagenesis.
Protein: DP03142 (UniProt Q16667)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 25–198 of KAP were visible in the electron density map; however, the N-terminal PEST sequence of ~23 residues was disordered.
Residues 23–200 were visible in the electron density maps, and the structure has been refined to final Rwork and Rfree of 20.2% and 25.4%, respectively (Table 2).
Cross-references: PDB:1FQ1
PDB:1FPZ
Protein: DP03142 (UniProt Q16667)
Region: residues 201	to 212
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 23–200 were visible in the electron density maps, and the structure has been refined to final Rwork and Rfree of 20.2% and 25.4%, respectively (Table 2).
Cross-references: PDB:1FQ1
PDB:1FPZ
Protein: DP03143 (UniProt P49327)
Region: residues 2344	to 2360
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As a result, a protein model could not be built for the following disordered regions: residues 2326–2328 (loop I, chain B only), 2344–2360 (loop II, both chains), 2450–2460 (loop III, both chains) and residues 2200–2220 and 2502–2510 on the N and C termini, respectively.
Cross-references: PDB:2PX6
Protein: DP03143 (UniProt P49327)
Region: residues 2200	to 2220
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As a result, a protein model could not be built for the following disordered regions: residues 2326–2328 (loop I, chain B only), 2344–2360 (loop II, both chains), 2450–2460 (loop III, both chains) and residues 2200–2220 and 2502–2510 on the N and C termini, respectively.
Cross-references: PDB:2PX6
Protein: DP03143 (UniProt P49327)
Region: residues 2344	to 2356
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the entire TE domain structure could be fitted into the electron density, except for the three segments and a glycine residue shown in Figs. ​Figs.1,1, ​,2,2, ​,3,3, with missing or weak density, indicating their high mobility. All of the disordered segments are in solvent-exposed regions and nowhere close to being involved in crystal contacts.
Cross-references: PDB:1XKT
Protein: DP03144 (UniProt Q05397)
Region: residues 565	to 583
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The majority of the structure is well defined, with the exception of the disordered activation loop (residues 565–583) and a short loop connecting β2 and β3 (residues 445–446) in the N-terminal domain
The αC helix is rotated away from the C-terminal lobe, and the activation loop is disordered, consistent with a lack of phosphorylation Figure 2, Figure 3, Figure 4.
Cross-references: PDB:1MP8
Protein: DP03144 (UniProt Q05397)
Region: residues 565	to 583
Annotation: molecular function activator activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The majority of the structure is well defined, with the exception of the disordered activation loop (residues 565–583) and a short loop connecting β2 and β3 (residues 445–446) in the N-terminal domain
Cross-references: PDB:1MP8
Protein: DP03145 (UniProt P29317)
Region: residues 761	to 777
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the structure is well defined, with the exception of residues 596–603 and 734–738 (the loop connecting β2 and β3) and the activation loop residues 760–883.
The lobes of EphA2 are in the open conformation, and the activation loop is disordered (Figure 2C).
Cross-references: PDB:1MQB
Protein: DP03145 (UniProt P29317)
Region: residues 760	to 883
Annotation: molecular function activator activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Most of the structure is well defined, with the exception of residues 596–603 and 734–738 (the loop connecting β2 and β3) and the activation loop residues 760–883.
The lobes of EphA2 are in the open conformation, and the activation loop is disordered (Figure 2C).
Cross-references: PDB:1MQB
Protein: DP03147 (UniProt Q86Y38)
Region: residues 232	to 251
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model is complete except for the disordered N-terminus (purification tag and XT1 residues 232-251) and two surface loops (XT1 residues 310-313 and 730-735). 
The N-terminus is disordered in the crystal structure of the apo form of XYLT1 (PDB:6FOA) but also in the structures where XYLT1 is complexed with peptides
Cross-references: PDB:6FOA
PDB:6EJ7
PDB:6EJ8
PDB:6EJA
PDB:6EJC
PDB:6EJE
Protein: DP03148 (UniProt P41227)
Region: residues 161	to 235
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure of the human NatE complex (NatA/Naa50) and NatE/HYPK complex shows this region of NAA10 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:6PPL
PDB:6PW9
EMDB:EMD-20442
EMDB:EMD-20501
Protein: DP03149 (UniProt Q9BXJ9)
Region: residues 573	to 639
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Using the helical numbering of the S. pombe structure, we did not observe electron density corresponding to the hNatA α33 and α34 helices, which are presumably disordered, and the loop-α40-loop segment of the hNaa15 C-terminus is only resolved in one of the protomer subunits due to stabilization by crystal packing.
Cross-references: PDB:6C9M
Protein: DP03149 (UniProt Q9BXJ9)
Region: residues 842	to 866
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Using the helical numbering of the S. pombe structure, we did not observe electron density corresponding to the hNatA α33 and α34 helices, which are presumably disordered, and the loop-α40-loop segment of the hNaa15 C-terminus is only resolved in one of the protomer subunits due to stabilization by crystal packing.
Cross-references: PDB:6C9M
Protein: DP03149 (UniProt Q9BXJ9)
Region: residues 574	to 637
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure of the human NatE complex (NatA/Naa50) and NatE/HYPK complex shows this region of  NAA15 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:6PPL
EMDB:EMD-20442
PDB:6PW9
EMDB:EMD-20501
Protein: DP03149 (UniProt Q9BXJ9)
Region: residues 842	to 866
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure of the human NatE complex (NatA/Naa50) and NatE/HYPK complex shows this region of NAA15 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:6PPL
PDB:6PW9
EMDB:EMD-20442
EMDB:EMD-20501
Protein: DP03150 (UniProt Q99598)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
TRAX also contains several extra loop sequences, of which the N-terminal 30 amino acids and amino acids 157–176 are disordered in the structure.
Cross-references: PDB:3PJA
PDB:3QB5
Protein: DP03150 (UniProt Q99598)
Region: residues 157	to 176
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
TRAX also contains several extra loop sequences, of which the N-terminal 30 amino acids and amino acids 157–176 are disordered in the structure.
Cross-references: PDB:3PJA
PDB:3QB5