LiteFold/DisProt huggingface dataset:
Protein: DP03512 (UniProt P18827)
Region: residues 23	to 254
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To experimentally estimate their amount of intrinsic disorder, the syndecan ectodomains were then analyzed by circular dichroism (Fig. 2A). The largest ectodomains, ED-1 and ED-3, were the most disordered (69 % of random coil), whereas the smallest ones, ED-2 and ED-4, contained 52 % and 44 % of random coil respectively (Fig. 2B). The content in α-helix of the four ectodomains was very low (<3 %), but they contained a significant amount of β-strands, which was higher in ED-2 and ED-4 (26 % and 33 % respectively) than in ED-1 and ED-3 (16 % and 17 % respectively) (Fig. 2B). β-strands were predicted to be located in the C-terminal half of ED-1 and ED-4 but distributed along ED-2 and ED-3 sequences (Supplementary Fig. S2A). Although they are extensively disordered, the syndecan EDs contain a significant amount of hydrophobic residues (37–52 %) of the total amino acid residues, which are usually depleted in IDPs [31].
Protein: DP03512 (UniProt P18827)
Region: residues 23	to 254
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The syndecan ectodomains are highly extended and flexible in solution
The four syndecan ectodomains were analyzed by SEC-small-angle X-ray scattering (SEC-SAXS) (Fig. 3 and Supplementary Fig. S4). ED-2 and the monomeric form of ED-4 had a similar radius of gyration (42.9 ± 0.33 Å and 41.53 ± 0.67 Å respectively), and a similar maximum intramolecular distance Dmax (185 Å and 180 Å respectively) (Table 1 and Supplementary Fig. S5).
The experimental values of the radius of gyration of the four ectodomains were close to the theoretical values calculated using the Flory’s equation for a random coil protein containing the same number of amino acid residues (Table 1). Furthermore, the Flory exponential scaling factors calculated for the syndecan EDs were 0.58 and 0.59, similar to the value calculated for chemically disordered proteins (0.60) which are more extended than IDPs [33].
The shape of the normalized Kratky plots of the four EDs (Fig. 3C) and of the ED4-dimer (Fig. 3D) was consistent with those of IDPs [35]. The Porod exponents of the EDs were similar (1.7 for ED-1, ED-3 and the monomer of ED-4, 1.8 for ED-2, and 1.9 for the dimer of ED-4) indicating that they all are flexible, the Porod exponent being equal to 2 for fully flexible systems [36]. The EDs flexibility was also demonstrated by the plateau observed in the Kratky-Debye plots (Fig. 3E). The syndecan ectodomains are thus disordered, flexible, and extended proteins in solution.
Protein: DP03512 (UniProt P18827)
Region: residues 23	to 254
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The hydrodynamic radius (Rh) of the ectodomains, determined by size-exclusion chromatography-dynamic light scattering (SEC-DLS), ranged from 34.1 Å (ED-2) to 50.1 Å (ED-3), and their Rg/Rh ratio, that provides information about protein shape and compactness, ranged from 1.16 (ED-4 monomer) to 1.31 (ED-4 dimer) (Table 1). These values were far higher than those of globular proteins (0.778) and close to those reported for prolate ellipsoids (1.36–2.24) [34] (Table 1).
Protein: DP03512 (UniProt P18827)
Region: residues 23	to 254
Annotation: disorder (Structural state)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Electrospray ionization-mass spectrometry (ESI-MS) in native conditions provides information on the variable degrees of compactness of IDPs. The charge state distributions (CSDs) determined by ESI-MS are related to the global compactness of proteins upon their transfer from solution to gas phase, the highest charge states corresponding to the most extended conformations [42]. The CSDs of the four ectodomains were trimodal, showing that the ectodomains of syndecans could adopt preferential conformations (Fig. 5A). Gaussian functions were fitted to the CSD envelopes to determine the relative proportions of the three major conformational ensembles. The most extended conformations (i.e. the highest charge states) were the most abundant for ED-1 (86 %), ED-2 (70 %) and ED-4 (85 %) but accounted for only 24 % for ED-3, in which the population with intermediate charge states predominated (Fig. 5B). Most compact conformations were found in minor amount for ED-1 (2 %), ED-2 (4 %), and ED-4 (8 %) and in larger amount for ED-3 (14 %).
Protein: DP03513 (UniProt P34741)
Region: residues 19	to 144
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03513 (UniProt P34741)
Region: residues 19	to 144
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03513 (UniProt P34741)
Region: residues 19	to 144
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To experimentally estimate their amount of intrinsic disorder, the syndecan ectodomains were then analyzed by circular dichroism (Fig. 2A). The largest ectodomains, ED-1 and ED-3, were the most disordered (69 % of random coil), whereas the smallest ones, ED-2 and ED-4, contained 52 % and 44 % of random coil respectively (Fig. 2B). The content in α-helix of the four ectodomains was very low (<3 %), but they contained a significant amount of β-strands, which was higher in ED-2 and ED-4 (26 % and 33 % respectively) than in ED-1 and ED-3 (16 % and 17 % respectively) (Fig. 2B). β-strands were predicted to be located in the C-terminal half of ED-1 and ED-4 but distributed along ED-2 and ED-3 sequences (Supplementary Fig. S2A). Although they are extensively disordered, the syndecan EDs contain a significant amount of hydrophobic residues (37–52 %) of the total amino acid residues, which are usually depleted in IDPs [31].
Protein: DP03513 (UniProt P34741)
Region: residues 19	to 144
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The syndecan ectodomains are highly extended and flexible in solution
The four syndecan ectodomains were analyzed by SEC-small-angle X-ray scattering (SEC-SAXS) (Fig. 3 and Supplementary Fig. S4). ED-2 and the monomeric form of ED-4 had a similar radius of gyration (42.9 ± 0.33 Å and 41.53 ± 0.67 Å respectively), and a similar maximum intramolecular distance Dmax (185 Å and 180 Å respectively) (Table 1 and Supplementary Fig. S5).
The experimental values of the radius of gyration of the four ectodomains were close to the theoretical values calculated using the Flory’s equation for a random coil protein containing the same number of amino acid residues (Table 1). Furthermore, the Flory exponential scaling factors calculated for the syndecan EDs were 0.58 and 0.59, similar to the value calculated for chemically disordered proteins (0.60) which are more extended than IDPs [33].
The shape of the normalized Kratky plots of the four EDs (Fig. 3C) and of the ED4-dimer (Fig. 3D) was consistent with those of IDPs [35]. The Porod exponents of the EDs were similar (1.7 for ED-1, ED-3 and the monomer of ED-4, 1.8 for ED-2, and 1.9 for the dimer of ED-4) indicating that they all are flexible, the Porod exponent being equal to 2 for fully flexible systems [36]. The EDs flexibility was also demonstrated by the plateau observed in the Kratky-Debye plots (Fig. 3E). The syndecan ectodomains are thus disordered, flexible, and extended proteins in solution.
Protein: DP03513 (UniProt P34741)
Region: residues 19	to 144
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The hydrodynamic radius (Rh) of the ectodomains, determined by size-exclusion chromatography-dynamic light scattering (SEC-DLS), ranged from 34.1 Å (ED-2) to 50.1 Å (ED-3), and their Rg/Rh ratio, that provides information about protein shape and compactness, ranged from 1.16 (ED-4 monomer) to 1.31 (ED-4 dimer) (Table 1). These values were far higher than those of globular proteins (0.778) and close to those reported for prolate ellipsoids (1.36–2.24) [34] (Table 1).
Protein: DP03513 (UniProt P34741)
Region: residues 19	to 144
Annotation: disorder (Structural state)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Electrospray ionization-mass spectrometry (ESI-MS) in native conditions provides information on the variable degrees of compactness of IDPs. The charge state distributions (CSDs) determined by ESI-MS are related to the global compactness of proteins upon their transfer from solution to gas phase, the highest charge states corresponding to the most extended conformations [42]. The CSDs of the four ectodomains were trimodal, showing that the ectodomains of syndecans could adopt preferential conformations (Fig. 5A). Gaussian functions were fitted to the CSD envelopes to determine the relative proportions of the three major conformational ensembles. The most extended conformations (i.e. the highest charge states) were the most abundant for ED-1 (86 %), ED-2 (70 %) and ED-4 (85 %) but accounted for only 24 % for ED-3, in which the population with intermediate charge states predominated (Fig. 5B). Most compact conformations were found in minor amount for ED-1 (2 %), ED-2 (4 %), and ED-4 (8 %) and in larger amount for ED-3 (14 %).
Protein: DP03514 (UniProt O75056)
Region: residues 47	to 387
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03514 (UniProt O75056)
Region: residues 47	to 387
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03514 (UniProt O75056)
Region: residues 47	to 387
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To experimentally estimate their amount of intrinsic disorder, the syndecan ectodomains were then analyzed by circular dichroism (Fig. 2A). The largest ectodomains, ED-1 and ED-3, were the most disordered (69 % of random coil), whereas the smallest ones, ED-2 and ED-4, contained 52 % and 44 % of random coil respectively (Fig. 2B). The content in α-helix of the four ectodomains was very low (<3 %), but they contained a significant amount of β-strands, which was higher in ED-2 and ED-4 (26 % and 33 % respectively) than in ED-1 and ED-3 (16 % and 17 % respectively) (Fig. 2B). β-strands were predicted to be located in the C-terminal half of ED-1 and ED-4 but distributed along ED-2 and ED-3 sequences (Supplementary Fig. S2A). Although they are extensively disordered, the syndecan EDs contain a significant amount of hydrophobic residues (37–52 %) of the total amino acid residues, which are usually depleted in IDPs [31].
Protein: DP03514 (UniProt O75056)
Region: residues 47	to 387
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The syndecan ectodomains are highly extended and flexible in solution
The four syndecan ectodomains were analyzed by SEC-small-angle X-ray scattering (SEC-SAXS) (Fig. 3 and Supplementary Fig. S4). ED-2 and the monomeric form of ED-4 had a similar radius of gyration (42.9 ± 0.33 Å and 41.53 ± 0.67 Å respectively), and a similar maximum intramolecular distance Dmax (185 Å and 180 Å respectively) (Table 1 and Supplementary Fig. S5).
The experimental values of the radius of gyration of the four ectodomains were close to the theoretical values calculated using the Flory’s equation for a random coil protein containing the same number of amino acid residues (Table 1). Furthermore, the Flory exponential scaling factors calculated for the syndecan EDs were 0.58 and 0.59, similar to the value calculated for chemically disordered proteins (0.60) which are more extended than IDPs [33].
The shape of the normalized Kratky plots of the four EDs (Fig. 3C) and of the ED4-dimer (Fig. 3D) was consistent with those of IDPs [35]. The Porod exponents of the EDs were similar (1.7 for ED-1, ED-3 and the monomer of ED-4, 1.8 for ED-2, and 1.9 for the dimer of ED-4) indicating that they all are flexible, the Porod exponent being equal to 2 for fully flexible systems [36]. The EDs flexibility was also demonstrated by the plateau observed in the Kratky-Debye plots (Fig. 3E). The syndecan ectodomains are thus disordered, flexible, and extended proteins in solution.
Protein: DP03514 (UniProt O75056)
Region: residues 47	to 387
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The hydrodynamic radius (Rh) of the ectodomains, determined by size-exclusion chromatography-dynamic light scattering (SEC-DLS), ranged from 34.1 Å (ED-2) to 50.1 Å (ED-3), and their Rg/Rh ratio, that provides information about protein shape and compactness, ranged from 1.16 (ED-4 monomer) to 1.31 (ED-4 dimer) (Table 1). These values were far higher than those of globular proteins (0.778) and close to those reported for prolate ellipsoids (1.36–2.24) [34] (Table 1).
Protein: DP03514 (UniProt O75056)
Region: residues 47	to 387
Annotation: disorder (Structural state)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Electrospray ionization-mass spectrometry (ESI-MS) in native conditions provides information on the variable degrees of compactness of IDPs. The charge state distributions (CSDs) determined by ESI-MS are related to the global compactness of proteins upon their transfer from solution to gas phase, the highest charge states corresponding to the most extended conformations [42]. The CSDs of the four ectodomains were trimodal, showing that the ectodomains of syndecans could adopt preferential conformations (Fig. 5A). Gaussian functions were fitted to the CSD envelopes to determine the relative proportions of the three major conformational ensembles. The most extended conformations (i.e. the highest charge states) were the most abundant for ED-1 (86 %), ED-2 (70 %) and ED-4 (85 %) but accounted for only 24 % for ED-3, in which the population with intermediate charge states predominated (Fig. 5B). Most compact conformations were found in minor amount for ED-1 (2 %), ED-2 (4 %), and ED-4 (8 %) and in larger amount for ED-3 (14 %).
Protein: DP03515 (UniProt P31431-2)
Region: residues 19	to 153
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03515 (UniProt P31431-2)
Region: residues 19	to 153
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03515 (UniProt P31431-2)
Region: residues 19	to 153
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To experimentally estimate their amount of intrinsic disorder, the syndecan ectodomains were then analyzed by circular dichroism (Fig. 2A). The largest ectodomains, ED-1 and ED-3, were the most disordered (69 % of random coil), whereas the smallest ones, ED-2 and ED-4, contained 52 % and 44 % of random coil respectively (Fig. 2B). The content in α-helix of the four ectodomains was very low (<3 %), but they contained a significant amount of β-strands, which was higher in ED-2 and ED-4 (26 % and 33 % respectively) than in ED-1 and ED-3 (16 % and 17 % respectively) (Fig. 2B). β-strands were predicted to be located in the C-terminal half of ED-1 and ED-4 but distributed along ED-2 and ED-3 sequences (Supplementary Fig. S2A). Although they are extensively disordered, the syndecan EDs contain a significant amount of hydrophobic residues (37–52 %) of the total amino acid residues, which are usually depleted in IDPs [31].
Protein: DP03515 (UniProt P31431-2)
Region: residues 19	to 153
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The syndecan ectodomains are highly extended and flexible in solution
The four syndecan ectodomains were analyzed by SEC-small-angle X-ray scattering (SEC-SAXS) (Fig. 3 and Supplementary Fig. S4). ED-2 and the monomeric form of ED-4 had a similar radius of gyration (42.9 ± 0.33 Å and 41.53 ± 0.67 Å respectively), and a similar maximum intramolecular distance Dmax (185 Å and 180 Å respectively) (Table 1 and Supplementary Fig. S5).
The experimental values of the radius of gyration of the four ectodomains were close to the theoretical values calculated using the Flory’s equation for a random coil protein containing the same number of amino acid residues (Table 1). Furthermore, the Flory exponential scaling factors calculated for the syndecan EDs were 0.58 and 0.59, similar to the value calculated for chemically disordered proteins (0.60) which are more extended than IDPs [33].
The shape of the normalized Kratky plots of the four EDs (Fig. 3C) and of the ED4-dimer (Fig. 3D) was consistent with those of IDPs [35]. The Porod exponents of the EDs were similar (1.7 for ED-1, ED-3 and the monomer of ED-4, 1.8 for ED-2, and 1.9 for the dimer of ED-4) indicating that they all are flexible, the Porod exponent being equal to 2 for fully flexible systems [36]. The EDs flexibility was also demonstrated by the plateau observed in the Kratky-Debye plots (Fig. 3E). The syndecan ectodomains are thus disordered, flexible, and extended proteins in solution.
Protein: DP03515 (UniProt P31431-2)
Region: residues 19	to 153
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The hydrodynamic radius (Rh) of the ectodomains, determined by size-exclusion chromatography-dynamic light scattering (SEC-DLS), ranged from 34.1 Å (ED-2) to 50.1 Å (ED-3), and their Rg/Rh ratio, that provides information about protein shape and compactness, ranged from 1.16 (ED-4 monomer) to 1.31 (ED-4 dimer) (Table 1). These values were far higher than those of globular proteins (0.778) and close to those reported for prolate ellipsoids (1.36–2.24) [34] (Table 1).
Protein: DP03515 (UniProt P31431-2)
Region: residues 19	to 153
Annotation: disorder (Structural state)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Electrospray ionization-mass spectrometry (ESI-MS) in native conditions provides information on the variable degrees of compactness of IDPs. The charge state distributions (CSDs) determined by ESI-MS are related to the global compactness of proteins upon their transfer from solution to gas phase, the highest charge states corresponding to the most extended conformations [42]. The CSDs of the four ectodomains were trimodal, showing that the ectodomains of syndecans could adopt preferential conformations (Fig. 5A). Gaussian functions were fitted to the CSD envelopes to determine the relative proportions of the three major conformational ensembles. The most extended conformations (i.e. the highest charge states) were the most abundant for ED-1 (86 %), ED-2 (70 %) and ED-4 (85 %) but accounted for only 24 % for ED-3, in which the population with intermediate charge states predominated (Fig. 5B). Most compact conformations were found in minor amount for ED-1 (2 %), ED-2 (4 %), and ED-4 (8 %) and in larger amount for ED-3 (14 %).
Protein: DP03516 (UniProt P30328)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unstructured N-terminal region of Major capsid protein of Paramecium bursaria Chlorella virus 1 (PBCV-1).
Cross-references: PDB:3KK5
EMDB:1662
Protein: DP03517 (UniProt P03437)
Region: residues 508	to 520
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 141-175 , including helices G and H, which in BHA form a compact unit adjacent to the five-stranded β- sheet and part of helix D, adopt in TBHA2 a more extended, partially disordered conformation running antiparallel to the coiled coil (Fig. 3b-d).
The soluble trimeric fragment considered here, TBHA2 , is prepared from Influenza A virus hemagglutinin at pH 5, since bound virus is internalized by endocytosis and the pH of endosomes is between pH 5 and pH 6.
An a-helix, H, in BHA (159-170) and five residues beyond it, 171-175, appear to be disordered in TBHA2.
Cross-references: PDB:1HTM
Protein: DP03517 (UniProt P03437)
Region: residues 508	to 520
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An a-helix, H, in BHA (159-170) and five residues beyond it, 171-175, appear to be disordered in TBHA2.
When incubated at the pH of fusion, BHA undergoes structural changes, two consequences of which are particularly important for investigations of the fusion-activated molecule. 
While TBHA2 is prepared from at pH 5, since bound virus is internalized by endocytosis and the pH of endosomes is between pH 5 and pH 6, BHA represents the Influenza A virus hemagglutinin at a physiological or cellular pH.
Cross-references: PDB:1HTM
Protein: DP03517 (UniProt P03437)
Region: residues 508	to 520
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 508-520 are folded in all the structures published.
Cross-references: PDB:2HMG
PDB:3HMG
PDB:4HMG
PDB:5HMG