LiteFold/DisProt huggingface dataset:
Protein: DP02456 (UniProt O35625)
Region: residues 31	to 59
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron densities of two Axin1 segments, Axin1(18-30) and Axin1(60-79), can be clearly visualized on the two ARC2 surfaces in the swapped TNKS dimers (Fig. S4). While the remaining parts of Axin1 cannot be seen in the electron density maps, these two Axin1 segments are likely from the same Axin1(1-80) molecule, since SEC results indicate that Axin1(1-80) stabilizes TNKS(308-655) dimerization in solution (Fig. S3), most likely by interacting with both copies of the swapped dimer. In addition, the distance between Axin1 G30 and A60 Cα atoms in our structure is 49.4 Å, which can be covered by the 29 missing residues in between
Cross-references: PDB:3UTM
Protein: DP02456 (UniProt O35625)
Region: residues 19	to 30
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Electron densities of two Axin1 segments, Axin1(18-30) and Axin1(60-79), can be clearly visualized on the two ARC2 surfaces in the swapped TNKS dimers (Fig. S4). While the remaining parts of Axin1 cannot be seen in the electron density maps, these two Axin1 segments are likely from the same Axin1(1-80) molecule, since SEC results indicate that Axin1(1-80) stabilizes TNKS(308-655) dimerization in solution (Fig. S3), most likely by interacting with both copies of the swapped dimer. In addition, the distance between Axin1 G30 and A60 Cα atoms in our structure is 49.4 Å, which can be covered by the 29 missing residues in between
The N-terminal domain of mouse Axin1, which contains residues 1-80, was shown to be responsible for TNKS binding, whereas residues 19-30, which is fully conserved in all Axin1 analogues, is necessary for this interaction
Cross-references: PDB:3UTM
Protein: DP02457 (UniProt O95400)
Region: residues 256	to 280
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structures of the U5-15K and GYF-domain are well defined in the electron density map except for some flexible regions in the C and/or N termini. The refined model of the U5-15K present in the complex consists of amino acid residues 3–137. The structure of the GYF-domain of U5-52K (residues 256–341) lacks the N-terminal 24 residues due to conformational flexibility.
Cross-references: PDB:1SYX
Protein: DP02458 (UniProt P17181)
Region: residues 49	to 58
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
missing residues in the PDB
Cross-references: PDB:3SE4
PDB:3S98
PDB:3SE3
Protein: DP02458 (UniProt P17181)
Region: residues 330	to 436
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The SD4 of IFNAR1 has been shown to be unnecessary for IFN binding (Lamken et al., 2005) and, consistent with electron-microscopic studies (Li et al., 2008), it was not visible in the electron density maps.
Cross-references: PDB:3SE4
PDB:3S98
PDB:3SE3
Protein: DP02460 (UniProt Q23985)
Region: residues 26	to 43
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Outside of the two WWE modules and the 12 C-terminal residues described above, electron density corresponding to the fairly long N- and C-terminal flanking sequences (17 and 60 residues, respectively; see the dashed regions in Figure 1B) is not interpretable, indicating that these two regions are disordered. This apparent disorder suggests that these terminal sequences might not be necessary for the structural integrity of the tandem WWE domain, despite moderate sequence conservation among Deltex orthologs
Cross-references: PDB:2A90
Protein: DP02460 (UniProt Q23985)
Region: residues 212	to 261
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Outside of the two WWE modules and the 12 C-terminal residues described above, electron density corresponding to the fairly long N- and C-terminal flanking sequences (17 and 60 residues, respectively; see the dashed regions in Figure 1B) is not interpretable, indicating that these two regions are disordered. This apparent disorder suggests that these terminal sequences might not be necessary for the structural integrity of the tandem WWE domain, despite moderate sequence conservation among Deltex orthologs
Cross-references: PDB:2A90
Protein: DP02461 (UniProt P17105)
Region: residues 185	to 202
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 185-202 at the N terminus and residue 459 at the C terminus were not seen in electron density and are presumed disordered in this structure.
Cross-references: PDB:1TZD
Protein: DP02463 (UniProt Q9NRR4)
Region: residues 390	to 411
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes two RIIIDs, dsRBD, and 53% of CED from DROSHA and two G1 helices from DGCR8. The model does not include N-terminal 21 residues, residues 459–521, 668–674, and 712–849 within CED, residues 930–957 in RIIIDa, and C-terminal 32 residues, because their electron densities are unclear or missing.
Cross-references: PDB:5B16
Protein: DP02463 (UniProt Q9NRR4)
Region: residues 459	to 521
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes two RIIIDs, dsRBD, and 53% of CED from DROSHA and two G1 helices from DGCR8. The model does not include N-terminal 21 residues, residues 459–521, 668–674, and 712–849 within CED, residues 930–957 in RIIIDa, and C-terminal 32 residues, because their electron densities are unclear or missing.
Cross-references: PDB:5B16
Protein: DP02463 (UniProt Q9NRR4)
Region: residues 712	to 849
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes two RIIIDs, dsRBD, and 53% of CED from DROSHA and two G1 helices from DGCR8. The model does not include N-terminal 21 residues, residues 459–521, 668–674, and 712–849 within CED, residues 930–957 in RIIIDa, and C-terminal 32 residues, because their electron densities are unclear or missing.
It is possible that the flexible regions such as PAZ-like domain or MB helix may be located closely to the UG or GHG elements.
The current structure covers most of the conserved regions of DROSHA except for the putative PAZ-like domain (residues 714–849, see below) (Figure 1A), whose electron density was insufficient to build a reliable model probably due to structural flexibility.
Cross-references: PDB:5B16
Protein: DP02463 (UniProt Q9NRR4)
Region: residues 930	to 957
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes two RIIIDs, dsRBD, and 53% of CED from DROSHA and two G1 helices from DGCR8. The model does not include N-terminal 21 residues, residues 459–521, 668–674, and 712–849 within CED, residues 930–957 in RIIIDa, and C-terminal 32 residues, because their electron densities are unclear or missing.
It is possible that the flexible regions such as PAZ-like domain or MB helix may be located closely to the UG or GHG elements.
Cross-references: PDB:5B16
Protein: DP02463 (UniProt Q9NRR4)
Region: residues 1333	to 1365
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The model does not include N-terminal 21 residues, residues 459–521, 668–674, and 712–849 within CED, residues 930–957 in RIIIDa, and C-terminal 32 residues, because their electron densities are unclear or missing.
Cross-references: PDB:5B16
Protein: DP02464 (UniProt Q12476)
Region: residues 147	to 159
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 147–159 of Air2p, a portion of the peptide linker between the fourth and fifth zinc knuckles, are disordered and were not modeled.
The linker acts as a spacer, allowing us to delete individual zinc knuckles while not shortening the distance between the remaining ones.
The fourth zinc knuckle (residues 123–136) is tethered to Trf4p via the adjacent linker region but has little direct contact with the surface of Trf4p.
Cross-references: PDB:3NYB
Protein: DP02464 (UniProt Q12476)
Region: residues 147	to 159
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 147–159 of Air2p, a portion of the peptide linker between the fourth and fifth zinc knuckles, are disordered and were not modeled.
The linker acts as a spacer, allowing us to delete individual zinc knuckles while not shortening the distance between the remaining ones.
The fourth zinc knuckle (residues 123–136) is tethered to Trf4p via the adjacent linker region but has little direct contact with the surface of Trf4p.
Cross-references: PDB:3NYB
Protein: DP02464 (UniProt Q12476)
Region: residues 147	to 159
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 147–159 of Air2p, a portion of the peptide linker between the fourth and fifth zinc knuckles, are disordered and were not modeled.
The linker acts as a spacer, allowing us to delete individual zinc knuckles while not shortening the distance between the remaining ones.
The fourth zinc knuckle (residues 123–136) is tethered to Trf4p via the adjacent linker region but has little direct contact with the surface of Trf4p.
Cross-references: PDB:3NYB
Protein: DP02465 (UniProt P07199)
Region: residues 583	to 599
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 16 residues of each CENP-B-(540-599) C terminus, which is the natural C terminus of the full-length CENP-B, are disordered. Therefore, they are not required for dimer formation. This may reflect the flexible nature of the CENP-B C-terminal region, which is rich in glycine residues.
Cross-references: PDB:1UFI
Protein: DP02466 (UniProt Q12432)
Region: residues 44	to 53
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the final model, the N-terminal six residues (numbered 1–6) and residues 44–53 were disordered.
Cross-references: PDB:3E9F
PDB:3E9G
Protein: DP02467 (UniProt P51617)
Region: residues 449	to 463
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Three regions are disordered in the structure, residues 243 to 247 in chain A and 244 to 248 in chain B at the loop between β3 and αC, residues 367 to 382 within the activation loop, and residues 449 to 460 in A and 449 to 463 in B at the long insertion between αG and αH (Fig. 3B). Despite being largely disordered, the IRAK1 activation loop is natively phosphorylated at S373, S375, S376, and T381, as shown by liquid chromatography tandem-mass spectrometry (LC/MS/MS) (Fig. S2). It should be noted that the disordered activation loop (residues 367 to 382) situates away from the inhibitor-binding site
Cross-references: PDB:6BFN
Protein: DP02467 (UniProt P51617)
Region: residues 367	to 382
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Three regions are disordered in the structure, residues 243 to 247 in chain A and 244 to 248 in chain B at the loop between β3 and αC, residues 367 to 382 within the activation loop, and residues 449 to 460 in A and 449 to 463 in B at the long insertion between αG and αH (Fig. 3B). Despite being largely disordered, the IRAK1 activation loop is natively phosphorylated at S373, S375, S376, and T381, as shown by liquid chromatography tandem-mass spectrometry (LC/MS/MS) (Fig. S2). It should be noted that the disordered activation loop (residues 367 to 382) situates away from the inhibitor-binding site
IRAK4 then phosphorylates IRAK1 to first prime its activity, enabling subsequent IRAK1 autophosphorylation in its activation loop to become fully activated
Cross-references: PDB:6BFN
Protein: DP02467 (UniProt P51617)
Region: residues 367	to 382
Annotation: phosphorylation display site (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Three regions are disordered in the structure, residues 243 to 247 in chain A and 244 to 248 in chain B at the loop between β3 and αC, residues 367 to 382 within the activation loop, and residues 449 to 460 in A and 449 to 463 in B at the long insertion between αG and αH (Fig. 3B). Despite being largely disordered, the IRAK1 activation loop is natively phosphorylated at S373, S375, S376, and T381, as shown by liquid chromatography tandem-mass spectrometry (LC/MS/MS) (Fig. S2). It should be noted that the disordered activation loop (residues 367 to 382) situates away from the inhibitor-binding site
IRAK4 then phosphorylates IRAK1 to first prime its activity, enabling subsequent IRAK1 autophosphorylation in its activation loop to become fully activated
Cross-references: PDB:6BFN
Protein: DP02468 (UniProt P17480)
Region: residues 547	to 560
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The first two N-terminal residues,including the first plasmid-encoded residue, and the C-terminal residues 547–560 are disordered.
Cross-references: PDB:2HDZ
Protein: DP02470 (UniProt Q12495)
Region: residues 457	to 519
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even though the entire 457–606 protein was present in the crystal (Figure 5A and data not shown), only amino acids 520–600 were visible in our electron density, and the 'wing' (576–581) was disordered.
Cross-references: PDB:5JBM
Protein: DP02471 (UniProt Q96G97)
Region: residues 2	to 60
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The typical transmembrane region is invisible in the EM map at the first sight. A close examination reveals that the densities of wheel outer ring are discontinuous, indicating that this region represents the TM region, which is invisible due to its flexibility or the C11 symmetry
The atomic model with 159 amino acids (149 amino acids were assigned side chain) was built for this region of each protomer according to the lumenal domain sequence of human SEIPIN. The final model is an undecamer with the lumenal domain alone, whose diameter is 160 Å
Cross-references: PDB:6DS5
Protein: DP02471 (UniProt Q96G97)
Region: residues 220	to 398
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The typical transmembrane region is invisible in the EM map at the first sight. A close examination reveals that the densities of wheel outer ring are discontinuous, indicating that this region represents the TM region, which is invisible due to its flexibility or the C11 symmetry
The atomic model with 159 amino acids (149 amino acids were assigned side chain) was built for this region of each protomer according to the lumenal domain sequence of human SEIPIN. The final model is an undecamer with the lumenal domain alone, whose diameter is 160 Å
Cross-references: PDB:6DS5
Protein: DP02472 (UniProt Q3U182)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CRTC2 residues 1–14 and 59–80 and CREB residues 283–284 and 338–341 are included in the expression construct, but are disordered in the structure.
Cross-references: PDB:5ZKO
Protein: DP02472 (UniProt Q3U182)
Region: residues 59	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CRTC2 residues 1–14 and 59–80 and CREB residues 283–284 and 338–341 are included in the expression construct, but are disordered in the structure.
Cross-references: PDB:5ZKO
Protein: DP02473 (UniProt Q15642)
Region: residues 289	to 303
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The models were built for residues 10–56 and 64–288 for EFCΔNCIP4 and residues 1–56 and 64–288 for EFCFBP17. The rest of the residues could not be modeled due to poor/disordered electron densities.
Cross-references: PDB:2EFK
Protein: DP02474 (UniProt Q12000)
Region: residues 283	to 319
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This included 17 groups comprising of Rbg1 (chain A 2–45, 53–125/131–174/233–299, 175–232, 300–369; chain B 2–53, 54–91/98–125/133–174/233–299, 175–232, 300–369) and Tma46 (chain C 214–240, 241–267, 268–282, 302–313, 314–338; chain D 214–240, 241–267, 268–282, 320–336).
Positions are referred to chain D
Cross-references: PDB:4A9A
Protein: DP02475 (UniProt Q86UE8)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
The first 200 amino acids of the N-terminus are predominantly disordered and are predicted to contain a nuclear localization signal (NLS).
Protein: DP02475 (UniProt Q86UE8)
Region: residues 1	to 190
Annotation: nucleus localization (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
We next examined the subcellular localization of these mutants and found that with the exception of the [increment]N-TLK2 mutant that contains the putative NLS, all of the mutants showed nuclear localization (Fig. 1f).
Cytoplasmic localization of the [increment]N-TLK2 mutant confirms the presence of the NLS in the N-terminus of the protein.
Protein: DP02476 (UniProt P36106)
Region: residues 1	to 231
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We also included models of the flexible Bye1 SPOC and PHD domains, with the latter positioned on the H3 tail emerging from the core nucleosome particle (Fig. 5C). Although the trajectory of the H3 tail is unclear and although the linkers between the Bye1 domains are flexible, the resulting model explained the position of the ChIP peak with high H3K4me3 occupancy.
In Bye1, the central TFIIS-like domain (TLD, residues 232–365) is flanked by an N-terminal plant homeo domain (PHD) (residues 74–134) and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain (residues 447–547)
flexible Bye1 PHD domain position: 74-134
Cross-references: PDB:4BY7
Protein: DP02476 (UniProt P36106)
Region: residues 74	to 134
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We also included models of the flexible Bye1 SPOC and PHD domains, with the latter positioned on the H3 tail emerging from the core nucleosome particle (Fig. 5C). Although the trajectory of the H3 tail is unclear and although the linkers between the Bye1 domains are flexible, the resulting model explained the position of the ChIP peak with high H3K4me3 occupancy.
In Bye1, the central TFIIS-like domain (TLD, residues 232–365) is flanked by an N-terminal plant homeo domain (PHD) (residues 74–134) and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain (residues 447–547)
Bye1 PHD domain contributes to chromatin association by binding trimethylated H3K4 peptides
The Bye1 PHD domain and full-length Bye1 bound specifically to H3K4me3 peptides (Fig. 4A). The high correlation between arrays probed with full-length Bye1 and the isolated PHD domain indicated that the histone-binding potential of Bye1 is harbored within its PHD domain
Additional functional data in vitro and in vivo indicate that Bye1 occupies active genes in their 5′-region and can bind to histone H3 tails with PTMs of active transcription using its PHD domain.
the flexible PHD domain is involved in histone-binding
Cross-references: PDB:4BY7
Protein: DP02476 (UniProt P36106)
Region: residues 134	to 232
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We also included models of the flexible Bye1 SPOC and PHD domains, with the latter positioned on the H3 tail emerging from the core nucleosome particle (Fig. 5C). Although the trajectory of the H3 tail is unclear and although the linkers between the Bye1 domains are flexible, the resulting model explained the position of the ChIP peak with high H3K4me3 occupancy.
Cross-references: PDB:4BY7
Protein: DP02476 (UniProt P36106)
Region: residues 366	to 447
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We also included models of the flexible Bye1 SPOC and PHD domains, with the latter positioned on the H3 tail emerging from the core nucleosome particle (Fig. 5C). Although the trajectory of the H3 tail is unclear and although the linkers between the Bye1 domains are flexible, the resulting model explained the position of the ChIP peak with high H3K4me3 occupancy.
Cross-references: PDB:4BY7
Protein: DP02476 (UniProt P36106)
Region: residues 366	to 594
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We also included models of the flexible Bye1 SPOC and PHD domains, with the latter positioned on the H3 tail emerging from the core nucleosome particle (Fig. 5C). Although the trajectory of the H3 tail is unclear and although the linkers between the Bye1 domains are flexible, the resulting model explained the position of the ChIP peak with high H3K4me3 occupancy.
flexible Bye1 SPOC domain position: 447-547
Cross-references: PDB:4BY7