LiteFold/DisProt huggingface dataset:
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues Mpa1-51, Pup1-20, Pup52-64 were also disordered in the crystal
structure of Pup:Mpa1-234 complex structure
Mpa46-51, Pup52-64 residues are
disordered in Mpa46-96:Pup21-64 complex structure.
Cross-references: PDB:3M91
Protein: DP00877 (UniProt P9WHN5)
Region: residues 51	to 64
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 52-64 residues of Pup were also disordered in the crystal, similar to what we observed in the Pup21-64:Mpa46-96 crystal structure; this unstructured region might serve as a flexible linker between the induced α-helix and the C-terminus that forms an isopeptide bond with a substrate.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 21	to 51
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Full-length Pup alone is randomly coiled and extended under physiologically relevant conditions in vitro. The randomly coiled state of Pup may increase its target capture radius, allowing it to find the proteasomal ATPase more easily. Once the C-terminal part of Pup contacts the Mpa coiled-coil, the pupylated substrate is “reeled” into the proteasomal ATPase, and the Pup N-terminus is gradually forced towards the OB channel in Mpa. The pulling of Pup’s N-terminus into the OB channel might subsequently pull the Pup helix away from the Mpa coiled-coil, causing Pup to unfold and thread further into the channel to reach the Mpa AAA region. This notion is supported by our structure demonstrating the displacement of the N-terminal half of the Pup helix (residues 21-30) from the Mpa coiled-coil (Fig. 2a-b), and by the observation that this region of Pup interacts more weakly with Mpa than the C-terminal half.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 21	to 51
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Based on our crystal structures and the existing biochemical data, we propose the following
mechanism of substrate recognition in the Pup-proteasome system (Fig. 3c): (I) Pup is
initially in an unfolded state when covalently linked to a protein substrate by its C-terminus via an isopeptide bond 15,16,18,21; (II) unstructured Pup folds into an α-helix, using the
Mpa coiled-coil as a template; and (III) the protein substrate, along with Pup, is pulled into
the central channel of the proteasomal ATPase at the expense of ATP hydrolysis 5,22. At the
interface between Mpa and the 20S core particle, Pup might either be removed by a
“depupylase” 23, or be pushed by Mpa further into the 20S core and degraded along with the
substrate.
Full-length Pup alone is
randomly coiled and extended under physiologically relevant conditions in vitro. The
randomly coiled state of Pup may increase its target capture radius, allowing it to find the
proteasomal ATPase more easily.
The Pup region extending from Ser21 to Ala51 folded into an α-helix, apparently using the
Mpa coiled-coil as a template.
Cross-references: PDB:3M9D
PDB:3M91
Protein: DP00877 (UniProt P9WHN5)
Region: residues 21	to 51
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Pup region extending from Ser21 to Ala51 folded into an α-helix, apparently using the
Mpa coiled-coil as a template.
The Pup helix interacted in an anti-parallel fashion with the lower half of the Mpa
coiled-coil (Fig. 1c). The Pup surface interacting with the Mpa coiled-coil was mainly
hydrophobic and involved two patches of leucine zipper-like interactions: a smaller patch
between Leu32 of Pup and Leu87 and Ala86 of Mpa-Ha; and an extensive patch formed by
Leu39, Leu40, Ile43, Val46, and Leu47 of Pup, Ala80, Leu73 of Mpa Ha, and Leu85,
Leu84, Ala80, and Leu77 of Mpa Hb (Fig. 1d).
Cross-references: PDB:3M9D
PDB:3M91
Protein: DP00877 (UniProt P9WHN5)
Region: residues 21	to 61
Annotation: protein binding (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
We used 1 H, 15 N HSQC experiments to test whether our Pup sample was functional for Mpa binding. S21–K61 attenuated upon Mpa addition and new Mpa-bound Pup resonances appeared
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 61
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As expected for a disordered protein, the chemical shift dispersion of 15 N is rather good, whereas amide 1 H chemical
shifts were dispersed over a narrow range from 7.8 to 8.6 p.p.m.,
which characterizes an unfolded protein.
Almost all of the heteronuclear NOEs are negative, indicating that most of the polypeptide chain adopts large amplitude ﬂuctuations on a subnanosecond time scale. This implies a highly ﬂexible state of Pup.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 30	to 59
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In the present paper, SPR (surface plasmon resonance) and NMR perturbation studies imply that the C-terminus of Pup, ranging from residues 30 to 59, binds
to Mpa probably through a hydrophobic interface.
At the same time, the weakening of
some other cross-peaks from residues in the region 32–55 was
observed (Figures 6A and 6B). Most of these perturbed residues
are hydrophobic, implying that Pup binds to Mpa via hydrophobic
interactions. This is consistent with the observations from the SPR
experiment.
The perturbed residues, most of
which are hydrophobic, are located in the region 30 to 59. These
observations suggest that Pup binds to Mpa via the last 30
amino acids, mainly through a hydrophobic interaction.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
We plotted the difference between the chemical shift values of Pup’s Cα and Hα atoms relative
to those of randomly coiled values applying sequence-dependent corrections 21 to find very
little deviation from the random coil values (Figure 2b). Only A51–A57 demonstrated a trend
towards helicity with slight, but consistent Cα downfield shifting and Hα upfield shifting
Compared to ubiquitin 22 , Pup exhibits significantly smaller hetNOE
values, with an average of 0.16 (at 800 MHz; Figure 4c) compared to ubiquitin’s average of
0.75 (at 750 MHz) 22 , thus revealing an increase of high frequency motions. Pup’s last three
C-terminal residues, its N-terminal end, and R29–K31 demonstrate enhanced flexible (Figure
4c). R29–K31 and V55–V59 exhibit faster than average R N (N X ) values (Figure 4b), providing
further evidence that these two regions undergo conformational exchange.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 52	to 64
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues Mpa1-51, Pup1-20, Pup52-64 were also disordered in the crystal
structure of Pup:Mpa1-234 complex structure
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The [ 15 N, 1 H]-HSQC spectrum of Pup shows poor dispersion
which is characteristic for an unfolded protein
We characterized the degree of ﬂexibility in the backbone of
Pup using the 15 N{ 1 H}-NOE experiment (Fig. 3b,c). Whereas the
N- and C-terminal residues show negative NOE values indicating
unrestricted motion of the N–H bond vector on the nanosecond
timescale, most residues of Pup have values between 0.2 and 0.4,
showing some degree of motional restriction of the backbone
(Fig. 3b and c). This conﬁrms that Pup is not entirely unstructured
in its free form.
15 N{ 1 H}-NOE experiment indicates that the protein
is partially structured, although it does not appear to occupy one
single favored conformation. Structure calculations using as input
the nearly complete resonance assignments and the NOESY spectra
do not converge to a single folded conformation. However, the res-
idues 50–58 adopt a helical conformation. Although this region
shows residual helical structure in these preliminary calculations,
the remainder of Pup occupies a range of conformations.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 21	to 58
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The observed
line-broadening clearly indicates interaction between Pup and
Mpa-CC. The most strongly affected 1 H– 15 N signals identify the
Mpa-CC binding region in Pup between residues 21 and 58.
Protein: DP00882 (UniProt G1TDB3)
Region: residues 1	to 39
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 (1-39) is missing but it was not mentioned in the article.
Cross-references: PDB:4KZX
PDB:4KZY
Protein: DP00882 (UniProt G1TDB3)
Region: residues 115	to 124
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 (115-124) is missing but it was not mentioned in the article.
Cross-references: PDB:4KZX
PDB:4KZY
Protein: DP00884 (UniProt P50106)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB corresponds to x-ray crystallographic evidence of the RNA polymerase I complex, form as a result of this protein interaction with multiple partners. The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:4C2M
Protein: DP00884 (UniProt P50106)
Region: residues 49	to 78
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB corresponds to x-ray crystallographic evidence of the RNA polymerase I complex, form as a result of this protein interaction with multiple partners. The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:4C2M
Protein: DP00884 (UniProt P50106)
Region: residues 101	to 137
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB corresponds to x-ray crystallographic evidence of the RNA polymerase I complex, form as a result of this protein interaction with multiple partners. The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:4C2M
Protein: DP00884 (UniProt P50106)
Region: residues 1	to 16
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:2RF4
Protein: DP00884 (UniProt P50106)
Region: residues 103	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:2RF4
Protein: DP00887 (UniProt P21246)
Region: residues 32	to 46
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with the previous study of PTN [27], we found that PTN is comprised of two TSR domains flanked by unstructured termini. Because no interdomain NOE was detected between the CTD and NTD, the two domains appear to be largely independent of each other and do not have a well-defined interdomain orientation.
The structured regions based on inspection of 2n6f are as follows: N-tail: 32-46; NTD (47-83), CTD (99-139), C-tail (140-168). The hinge region that is not constrained to the CTD corresponds to residues: 84-95. Numbering in the paper does not follow UNIPROT numbering. i.e. F63 corresponds to F95 and K60-K61 corresponds to UNIPROT: K92, K93.
Cross-references: PDB:2N6F
Protein: DP00887 (UniProt P21246)
Region: residues 140	to 168
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with the previous study of PTN [27], we found that PTN is comprised of two TSR domains flanked by unstructured termini. Because no interdomain NOE was detected between the CTD and NTD, the two domains appear to be largely independent of each other and do not have a well-defined interdomain orientation.
The structured regions based on inspection of 2n6f are as follows: N-tail: 32-46; NTD (47-83), CTD (99-139), C-tail (140-168). The hinge region that is not constrained to the CTD corresponds to residues: 84-95. Numbering in the paper does not follow UNIPROT numbering. i.e. F63 corresponds to F95 and K60-K61 corresponds to UNIPROT: K92, K93.
Cross-references: PDB:2N6F
Protein: DP00887 (UniProt P21246)
Region: residues 84	to 95
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with the previous study of PTN [27], we found that PTN is comprised of two TSR domains flanked by unstructured termini. Because no interdomain NOE was detected between the CTD and NTD, the two domains appear to be largely independent of each other and do not have a well-defined interdomain orientation.
Definitive NOE cross-peaks between CTD and residues in the hinge segment connecting the two TSR domains (residues 58–66) can be observed. Specifically, aromatic protons of F63 can be seen contacting side chains of Y69, V103 and I105 (Fig. 1D). Because F63 is the only residue with significant contacts with the CTD and the tolerance in these distance constraints is relatively large, the hinge shows larger positional variation than the TSR domains.
The structured regions based on inspection of 2n6f are as follows: N-tail: 32-46; NTD (47-83), CTD (99-139), C-tail (140-168). The hinge region that is not constrained to the CTD corresponds to residues: 84-95. Numbering in the paper does not follow UNIPROT numbering. i.e. F63 corresponds to F95 and K60-K61 corresponds to UNIPROT: K92, K93.
Cross-references: PDB:2N6F
Protein: DP00887 (UniProt P21246)
Region: residues 84	to 95
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our structure shows that PTN possesses large basic surfaces on both of its structured domains and also that residues in the hinge segment connecting the domains have significant contacts with the C-terminal domain. Our analysis of PTN–CS interactions showed that the C-terminal tail of PTN is essential for maintaining stable interactions with chondroitin sulfate A, the type of CS commonly found on PTPRZ.
Definitive NOE cross-peaks between CTD and residues in the hinge segment connecting the two TSR domains (residues 58–66) can be observed. Specifically, aromatic protons of F63 can be seen contacting side chains of Y69, V103 and I105 (Fig. 1D). Because F63 is the only residue with significant contacts with the CTD and the tolerance in these distance constraints is relatively large, the hinge shows larger positional variation than the TSR domains.
The structured regions based on inspection of 2n6f are as follows: N-tail: 32-46; NTD (47-83), CTD (99-139), C-tail (140-168). The hinge region that is not constrained to the CTD corresponds to residues: 84-95. Numbering in the paper does not follow UNIPROT numbering. i.e. F63 corresponds to F95 and K60-K61 corresponds to UNIPROT: K92, K93.
Cross-references: PDB:2N6F
Protein: DP00887 (UniProt P21246)
Region: residues 147	to 168
Annotation: carbohydrate binding (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
Our analysis of PTN–CS interactions showed that the C-terminal tail of PTN is essential for maintaining stable interactions with chondroitin sulfate A, the type of CS commonly found on PTPRZ.
Furthermore, studies have also shown that truncated PTN missing the C-terminal tail (residues 115–136) can be found in vivo in significant quantities but is incapable of signaling through PTPRZ [35–37]. In addition, peptides derived from the C-terminal tail of PTN can inhibit PTPRZ-dependent cell migration [38]. This implies that the C-terminal tail, which does not contribute to heparin binding, plays an important role in interactions with PTPRZ.
However, truncated PTN failed to bind to CSA entirely, whereas wild-type PTN binds CSA with high affinity (Kd ~ 17 nM). These data indicate that the Cterminal tail of PTN is crucial for maintaining strong interactions with CSA, the type of CS commonly found on PTPRZ.
Work reported in the present study shows that, although the C-terminal tail plays a minimal role in binding the highly sulfated CSE, it is vital for maintaining stable interactions with CSA. Because more than 90% of disaccharides in the GAG chains of PTPRZ are CSA disaccharides [42], the Cterminal tail of PTN is demonstrated to be a crucial mediator of the interaction of PTN with PTPRZ. 
The C-terminal truncation: residues 115-136 discussed by the authors corresponds to residues 147-168 of the Uniprot entry
Protein: DP00887 (UniProt P21246)
Region: residues 147	to 168
Annotation: carbohydrate binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Our analysis of PTN–CS interactions showed that the C-terminal tail of PTN is essential for maintaining stable interactions with chondroitin sulfate A, the type of CS commonly found on PTPRZ.
Furthermore, studies have also shown that truncated PTN missing the C-terminal tail (residues 115–136) can be found in vivo in significant quantities but is incapable of signaling through PTPRZ [35–37]. In addition, peptides derived from the C-terminal tail of PTN can inhibit PTPRZ-dependent cell migration [38]. This implies that the C-terminal tail, which does not contribute to heparin binding, plays an important role in interactions with PTPRZ.
In the absence of the Cterminal tail, CTD residues bound CSA dp8 with a Kd of only ~ 320 µM. Similarly, the CSA dp8 binding Kd of the NTD also doubled to 1.2 mM. This indicates that removal of the C-terminal tail has a significant effect on the affinity of PTN for CSA dp8 and is consistent with the results of the ELISA. It should be noted that the inability of truncated PTN to bind native CSA in ELISA does not contradict the results of the NMR titrations. The discrepancy can be explained by the successive washes required in ELISA, which prevents weak interactions 
Work reported in the present study shows that, although the C-terminal tail plays a minimal role in binding the highly sulfated CSE, it is vital for maintaining stable interactions with CSA. Because more than 90% of disaccharides in the GAG chains of PTPRZ are CSA disaccharides [42], the Cterminal tail of PTN is demonstrated to be a crucial mediator of the interaction of PTN with PTPRZ. 
The C-terminal truncation: residues 115-136 discussed by the authors corresponds to residues 147-168 of the Uniprot entry
Protein: DP00887 (UniProt P21246)
Region: residues 144	to 168
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
PTN112–136 inhibited binding of PTN to anb3 integrin, and as shown by surface plasmon resonance (SPR) measurements, specifically interacted with the specificity loop of the extracellular domain of b3. Moreover, it abolished PTN-induced FAK Y397 phosphorylation, similarly to the effect of a neutralizing anb3-selective antibody
PTN112_136 AFFECTED THE INTERACTION OF PTN WITH  anb3 INTEGRIN. Since both RPTPb/z and anb3 integrin are required for PTN-induced HUVEC migration [Polykratis et al., 2005; Mikelis et al., 2009], we studied whether PTN112–136 affects interaction of PTN with alphav b3, RPTPb/z, or both. Cells were grown in the presence or absence of PTN112–136 and in each case, 3mg of total protein from cell lysates were immunoprecipitated for anb3 or RPTPb/z and analyzed for the presence of PTN. PTN112–136 inhibited interaction of PTN with anb3 (Fig. 3A) but not RPTPb/z (Fig. 3B) in HUVEC.
The numbering by the authors differs from the uniprot numbering. Residue 112-136 correspond to 144-168 of the uniprot numbering.
Protein: DP00887 (UniProt P21246)
Region: residues 144	to 168
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
PTN112–136 inhibited binding of PTN to anb3 integrin, and as shown by surface plasmon resonance (SPR) measurements, specifically interacted with the specificity loop of the extracellular domain of b3. Moreover, it abolished PTN-induced FAK Y397 phosphorylation, similarly to the effect of a neutralizing anb3-selective antibody
PTN112_136 SPECIFICALLY INTERACTED WITH THE CYSTEINE LOOP 177–184 OF THE b3 INTEGRIN EXTRACELLULAR DOMAIN. Since PTN interacts with anb3 through the specificity loop of the b3 integrin extracellular domain [Mikelis et al., 2009], we studied the interaction of PTN112–136 with a synthetic peptide that corresponds to aminoacids 177–184 and mimics the cysteine loop of b3 (B3 peptide) by using surface plasmon resonance (SPR)
Typical analyte–receptor binding kinetics are presented in Figure 4B. PTN112–136 and B3 peptide formed a relatively high affinity complex. The affinity of B3 peptide for PTN112–136 was much higher than the affinity of the B3 scrambled peptide.
In the present study, we show that the C-terminal region of PTN is responsible for binding to the Cys-loop of the b3 subunit, playing a major role in the interaction of PTN with anb3 and the resulting stimulation of cell migration.
The numbering by the authors differs from the uniprot numbering. Residue 112-136 correspond to 144-168 of the uniprot numbering.