LiteFold/DisProt huggingface dataset:
Protein: DP02392 (UniProt Q9ZVD0)
Region: residues 435	to 444
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
Protein: DP02392 (UniProt Q9ZVD0)
Region: residues 366	to 380
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
Protein: DP02393 (UniProt Q8IZD2)
Region: residues 323	to 339
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Molecule B had well defined electron density for SET core, however residues 327 to 339 at the N-terminus and 449 to the end at the C-terminus were disordered and could not be modeled from X-ray data.
Cross-references: PDB:5HT6
Protein: DP02395 (UniProt P35201)
Region: residues 365	to 436
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model included density for residues 437–530 (Figure 3), but residues 365–436 were not visible, implying that they were disordered
Cross-references: PDB:2VPV
Protein: DP02395 (UniProt P35201)
Region: residues 331	to 438
Annotation: localization (Biological process)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model included density for residues 437–530 (Figure 3), but residues 365–436 were not visible, implying that they were disordered
Two of the five regions of Mif2p were found to be essential for function: those between residues 267 and 347, a segment that contains the CENP-C signature box (green; Figure 1), and those between 331 and 438. These regions contain the likely nuclear localization sequence (QRRKKQKK; Nair and Rost, 2005 blue right-pointing triangle), but we did not explicitly test whether the sequence is essential for correct localization.
Cross-references: PDB:2VPV
Protein: DP02396 (UniProt Q7RTP6)
Region: residues 1881	to 1990
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:5SZG
Protein: DP02396 (UniProt Q7RTP6)
Region: residues 1735	to 1918
Annotation: protein binding (Molecular function)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
The minimum region of MICAL3 required for the binding of MKLP1 corresponds to the deletion mutant MICAL3-CC4 (Fig. 2A, 2B) that spans amino acids 1735-1918
Taken together, our results show that MKLP1 and MICAL3 primarily interact through the unstructured polypeptide region in MKLP1 and the C-terminal coiled-coil domain of MICAL3, with additional contacts provided by the second coiled-coil domain of MICAL3 and the coiled-coil domain of MKLP1
MICAL3 Interacts with MKLP1
Protein: DP02396 (UniProt Q7RTP6)
Region: residues 1735	to 1918
Annotation: localization (Biological process)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
The minimum region of MICAL3 required for the binding of MKLP1 corresponds to the deletion mutant MICAL3-CC4 (Fig. 2A, 2B) that spans amino acids 1735-1918
Taken together, our results show that MKLP1 and MICAL3 primarily interact through the unstructured polypeptide region in MKLP1 and the C-terminal coiled-coil domain of MICAL3, with additional contacts provided by the second coiled-coil domain of MICAL3 and the coiled-coil domain of MKLP1
MICAL3 Interacts with MKLP1
We showed that MKLP1 recruits MICAL3 to the central spindle, whereas MICAL3 participates in targeting to the midbody its binding partners ELKS and Rab8A, and the loss of both ELKS and Rab8A also caused cytokinesis defects.
We conclude that MICAL3 can form a triple complex with MKLP1 and ELKS and through the interaction with the former, target the latter to the midbody.
In a mechanism independent of its enzymatic activity, MICAL3 targets the adaptor protein ELKS and Rab8A-positive vesicles to the midbody, and the depletion of ELKS and Rab8A also leads to cytokinesis defects.
We propose that MICAL3 acts as a midbody-associated scaffold for vesicle targeting, which promotes maturation of the intercellular bridge and abscission.
MICAL3 is required for ELKS localization to the midbody.
Protein: DP02396 (UniProt Q7RTP6)
Region: residues 1735	to 1918
Annotation: molecular adaptor activity (Molecular function)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
We conclude that MICAL3 can form a triple complex with MKLP1 and ELKS and through the interaction with the former, target the latter to the midbody
Protein: DP02397 (UniProt P11746)
Region: residues 2	to 17
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No interpretable electron density for MCM1 cis residues 2–14 and trans residues 2–17 was observed, and we presume that these residues are disordered in the crystal. These N-terminal residues are not necessary for cell-type-specific transcription or viability, but appear to be involved in a phosphorylation-dependent manner in the yeast cell's response to stress, for example high salt concentrations
Cross-references: PDB:1MNM
Protein: DP02397 (UniProt P11746)
Region: residues 2	to 17
Annotation: phosphorylation display site (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No interpretable electron density for MCM1 cis residues 2–14 and trans residues 2–17 was observed, and we presume that these residues are disordered in the crystal. These N-terminal residues are not necessary for cell-type-specific transcription or viability, but appear to be involved in a phosphorylation-dependent manner in the yeast cell's response to stress, for example high salt concentrations
Cross-references: PDB:1MNM
Protein: DP02397 (UniProt P11746)
Region: residues 2	to 17
Annotation: molecular sequestering activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No interpretable electron density for MCM1 cis residues 2–14 and trans residues 2–17 was observed, and we presume that these residues are disordered in the crystal. These N-terminal residues are not necessary for cell-type-specific transcription or viability, but appear to be involved in a phosphorylation-dependent manner in the yeast cell's response to stress, for example high salt concentrations
Cross-references: PDB:1MNM
Protein: DP02397 (UniProt P11746)
Region: residues 2	to 17
Annotation: phosphorylation display site (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
two major phosphorylation sites lie in the N-terminal 17 amino acids
both S2 and T8 are phosphorylation sites
Protein: DP02398 (UniProt Q04637)
Region: residues 592	to 606
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the Hs complex, the equivalent N-terminal eIF4G residues (Q592–L606) were not visible in the electron density map, suggesting either high flexibility or susceptibility to proteolytic degradation during crystallization.
Cross-references: PDB:5T46
Protein: DP02398 (UniProt Q04637)
Region: residues 161	to 216
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N HSQC spectrum of 15N-Nt4G displays poorly dispersed signals, particularly in the 1H dimension, which suggests that the eIF4G fragment is not structured in solution (Figure 2D).
Protein: DP02398 (UniProt Q04637)
Region: residues 178	to 202
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon addition of RRM2, the Nt4G signals became widely dispersed, indicating that the polypeptide folds upon binding to RRM2 (Figure 2E). Backbone assignments of 13C,15N-labeled Nt4G alone and in complex with RRM2 showed that eIF4G residues from Lys178 to Thr202 were affected by RRM2 binding (Figure 2F). No chemical shift changes were observed for the N- and C-terminal residues, suggesting that they do not participate in binding RRM1-2. The large magnitude of the changes (up to 1.56 ppm) reflects the dramatic change from a flexible polypeptide to a rigid, structured conformation in the complex (Figures 2D–2F).
Cross-references: PDB:4F02
Protein: DP02398 (UniProt Q04637)
Region: residues 178	to 203
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, NMR titrations of 15N-RRM2 (PABP residues 86–192) with the eIF4G fragment led to specific chemical shift changes of the 1H,15N HSQC signals.
Backbone assignments of 13C,15N-labeled Nt4G alone and in complex with RRM2 showed that eIF4G residues from Lys178 to Thr202 were affected by RRM2 binding (Figure 2F). 
The spectra identify residues 178–203 as the region of eIF4G that binds RRM2.
Protein: DP02398 (UniProt Q04637)
Region: residues 179	to 198
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In both structures, we observed electron density for PABP residues 10–183, nine adenosine nucleotides, and residues 179-198 of eIF4G. The eIF4G peptide adopts a secondary structure of two short b strands and one a helix bound to PABP RRM2 (Figure 3A).
Cross-references: PDB:4F02
Protein: DP02398 (UniProt Q04637)
Region: residues 161	to 216
Annotation: positive regulation of eukaryotic translation initiation factor 4F complex assembly (Biological process)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In the presence of Nt4G, the RRM1-2·poly(A) interaction was enhanced, and a supershifted ternary complex was observed. The enhancement of RNA binding was also observed with RRM1-2-3-4 binding to 32P-labeled poly(A)25. Quantification of the amount of poly(A) bound to RRM1-2-3-4 shows that the presence of Nt4G increases the affinity of the RRMs for poly(A) by at least 10-fold (Figure 4B).
Protein: DP02398 (UniProt Q04637)
Region: residues 179	to 198
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In both structures, we observed electron density for PABP residues 10–183, nine adenosine nucleotides, and residues 179-198 of eIF4G. The eIF4G peptide adopts a secondary structure of two short b strands and one a helix bound to PABP RRM2 (Figure 3A).
Cross-references: PDB:4F02
Protein: DP02398 (UniProt Q04637)
Region: residues 161	to 216
Annotation: positive regulation of eukaryotic translation initiation factor 4F complex assembly (Biological process)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To quantify the cooperativity, we measured the binding affinities using ITC. In agreement with the gel shift studies, we found that poly(A)11 binds to the RRM1-2·Nt4G complex with 10-fold better affinity than to RRM1-2, 62 nM and 0.6 μM, respectively (Figure 4C).
Protein: DP02398 (UniProt Q04637)
Region: residues 161	to 216
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To quantify the cooperativity, we used ITC to measure the affinities of eIF4G for RRM2, RRM1-2, and RRM2-3. Comparison of the affinities of RRM1-2 and RRM2 showed that RRM1 decreased the affinity in the absence of poly(A) RNA. Under identical conditions, PABP RRM2 bound Nt4G with 3-fold better affinity than RRM1-2, Kd of 5 μM and 19 μM, respectively (Figure 5C).
Protein: DP02398 (UniProt Q04637)
Region: residues 161	to 216
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
We carried out coimmunoprecipitation (coIP) assays on HeLa cell extracts to test the role of RNA on the PABP·eIF4G interaction in cells (Figure 6). Endogenous eIF4G could be immunoprecipitated with an anti-PABP antibody (Figure 6B).
Protein: DP02398 (UniProt Q04637)
Region: residues 1427	to 1436
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal region of human eIF4GI consists of two a-helical domains, 4G/C1 and 4G/C2, joined by a 13 residue linker (Figures 1B and 2).
The linker connecting domains 4G/C1 and 4G/C2 is both highly polar and apparently flexible (10/13 residues were not visible in our electron density maps).
Ten residues in the interdomain linker of 4G/C (left) were not observed in the electron density maps and are shown as a polyalanine trace (violet).
At the final stages of refinement, NCS operators were re-evaluated, and restrained NCS refinement yielded a final model (residues
1234–1566, excluding 1428–1437 from the interdomain linker, rmsd = 0.2 A˚ for 323 a-carbon pairs) with an R factor of 24.4% and an R free of 29.2% (Table 1).
The authors used isoform 8 (DP03499) in their experiments, which is 1 residue longer than isoform A. Thus, region 1428-1437 corresponds to region 1427-1436 of the canonical UniProt sequence. The sequence of the disordered region is identical in both isoforms.
Cross-references: PDB:1UG3
Protein: DP02398 (UniProt Q04637)
Region: residues 1427	to 1436
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal region of human eIF4GI consists of two a-helical domains, 4G/C1 and 4G/C2, joined by a 13 residue linker (Figures 1B and 2).
The linker connecting domains 4G/C1 and 4G/C2 is both highly polar and apparently flexible (10/13 residues were not visible in our electron density maps).
Ten residues in the interdomain linker of 4G/C (left) were not observed in the electron density maps and are shown as a polyalanine trace (violet).
At the final stages of refinement, NCS operators were re-evaluated, and restrained NCS refinement yielded a final model (residues
1234–1566, excluding 1428–1437 from the interdomain linker, rmsd = 0.2 A˚ for 323 a-carbon pairs) with an R factor of 24.4% and an R free of 29.2% (Table 1).
The authors used isoform 8 (DP03499) in their experiments, which is 1 residue longer than isoform A. Thus, region 1428-1437 corresponds to region 1427-1436 of the canonical UniProt sequence. The sequence of the disordered region is identical in both isoforms.
Cross-references: PDB:1UG3
Protein: DP02398 (UniProt Q04637)
Region: residues 1079	to 1233
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Sequence comparisons (Figure 1A), secondary structure predictions (data not shown), and limited proteolysis combined with mass spectrometry (data not shown) permitted identification of a protease-resistant C-terminal portion of human eIF4GI that supports binding to eIF4A and Mnk1 (data not shown). Further truncation (eIF4GI[1235–1572]) yielded a two-domain protein that gives high-quality crystals with two protomers per asymmetric unit (Experimental Procedures).
Limited proteolysis of the C-terminal region of human eIF4GI (residues 1080–1600) with a panel of specific endoproteases yielded a resistant core of approximately 40 kDa, as judged by gel electrophoresis (data not shown). Matrix-assisted laser desorption ionization mass spectrometry and N-terminal sequencing of proteolytic fragments mapped a large number of proteolytic cleavage sites to residues 1080–1234.
The authors used isoform 8 (DP03499) in their experiments, which is 1 residue longer than isoform A. Thus, region 1080-1234 corresponds to region 1079-1233 of the canonical UniProt sequence. The sequence of the disordered region is identical in both isoforms.
Protein: DP02398 (UniProt Q04637)
Region: residues 290	to 754
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 It is likely that other domains of eIF4G, not visible in this work because of possible flexibility, could also make interactions with nearby subunits such as the eIF3d-NTT and eIF3e, which has been previously suggested by biochemical cross-linking (4).
The Cryo-EM structure of the 48S translational initiation complex shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:6ZMW
Protein: DP02398 (UniProt Q04637)
Region: residues 992	to 1599
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 It is likely that other domains of eIF4G, not visible in this work because of possible flexibility, could also make interactions with nearby subunits such as the eIF3d-NTT and eIF3e, which has been previously suggested by biochemical cross-linking (4).
The Cryo-EM structure of the 48S translational initiation complex shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:6ZMW
Protein: DP02399 (UniProt P06730)
Region: residues 1	to 29
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal Regions of Hs and Dm eIF4E Are Not Required for Binding to eIF4G
Although full-length eIF4E was used in the human complex, the first 29 residues (M1–A29) are not visible in the electron density map
Cross-references: PDB:5T46
Protein: DP02399 (UniProt P06730)
Region: residues 2	to 35
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this NMR ensemble of the apo-eIF4E, the loops S1–S2, H2–S3, H4–S5 and S7–S8 are less defined while the first 35 residues at the N-terminus are completely disordered.
The authors mention in the Results and discussion section that the N-terminal methionine is removed from the protein: As can be seen in Figure 2A, the molecular mass of eIF4E is 24964.373.2 Da slightly less than the predicted mass 25097.2 Da. This mass difference (132.9 Da) corresponds to the loss of methionine (131.2 Da) at the N-terminus, which is a common event (Huang et al, 1987). The absence of Met1 in the NMR data corroborates this hypothesis.
Cross-references: PDB:2GPQ
Protein: DP02399 (UniProt P06730)
Region: residues 1	to 26
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The present results provide the structural basis for the biological function of both N- and C-terminal mobile regions of eIF4E in translation initiation, especially the regulatory function through the switch-on/off of eIF4E-binding protein–eIF4E phosphorylation.
However, the structures of the N- and C-terminal regions are still unclear, because of the high flexibility of these regions in eIF4E.
As is shown in Figure 1, we could determine the structure from Glu27 (in both complexes of human full-length eIF4E; it was impossible to determine the structure from the N-terminus to Gln26 because of the high flexibility.
In contrast with large flexibility at both N- and C-terminal regions, the core regions consisting of eight-stranded anti-parallel b-sheets and three long a-helices are very similar to each other.
Cross-references: PDB:1IPB
PDB:1IPC
Protein: DP02400 (UniProt P48598)
Region: residues 1	to 68
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal unstructured regions of metazoan eIF4Es
Cross-references: PDB:5T48
PDB:5T47
Protein: DP02401 (UniProt O61380)
Region: residues 633	to 660
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the N-terminal region establishes a stabilizing network of intramolecular hydrogen bonds (Figure 3H) and likely undergoes a disorder-to-order transition when binding to eIF4E.
Cross-references: PDB:5T48
Protein: DP02401 (UniProt O61380)
Region: residues 578	to 601
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the eIF4G-eIF4E complex, only the canonical motif and additional short N- and C-terminal extensions were observed (Figures 1H and S2B–S2F). The auxiliary VKNVSI was not visible in our structure, suggesting that it may form transient interactions or may be susceptible to proteolysis.
Cross-references: PDB:4UEC
Protein: DP02401 (UniProt O61380)
Region: residues 638	to 650
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the eIF4G-eIF4E complex, only the canonical motif and additional short N- and C-terminal extensions were observed (Figures 1H and S2B–S2F). The auxiliary VKNVSI was not visible in our structure, suggesting that it may form transient interactions or may be susceptible to proteolysis.
Cross-references: PDB:4UEC
Protein: DP02404 (UniProt Q96N21)
Region: residues 136	to 153
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Together these data suggest that additional amino acids beyond residue 136 in the longer construct are disordered and the tepsin ENTH domain is indeed smaller than other published ENTH structures by two α-helices.
Cross-references: PDB:5WF9
Protein: DP02405 (UniProt Q8IYW5)
Region: residues 94	to 111
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The overall structure of RNF168N-111 contains ordered residues from L3 to S93. The residues from G94 to S111 could not be observed in the electron density map, indicating high flexibility of this region
Cross-references: PDB:4GB0