LiteFold/DisProt huggingface dataset:
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: molecular function regulator (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
We show by cryoelectron microscopy (cryo-EM) and allied methods that simian tetherin is targeted in a unique way by the induced refolding of the b subunit of AP-2 from an a-helix to a b-hairpin, creating a binding site for the (G/D)DIWK motif in a crevice between the new b-hairpin and Nef
However, when bound to both tetherin and Nef, b2 (peptide 7–18) underwent 40% less HD exchange (30 s) (Figures 4C and S4A). Slower deuteration was also seen in a and s2 residues in SIVsmm Nef binding regions (Figures S4B and S4C), as expected. The finding that protection from amide HD exchange in the b2 N terminus depends on the presence of both SIVsmm Nef and tetherin strongly supports the conclusions drawn from the cryo-EM structure, which shows that the presence of these two molecules together is required for refolding of this region
We used fluorescence polarization (FP) to determine that Alexa488-tetherin tail bound to AP2DmC and SIVsmm Nef with Kd = 2.7 mM ± 0.1 mM (Figures 1C and 1D), while binding to the separate components or to AP2hemi was undetectable. These data indicate that simian tetherin binds to the AP-2 core and SIVsmm Nef in a cooperative and high-affinity ternary complex that requires elements of the full AP-2 tetramer
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: molecular function regulator (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
We show by cryoelectron microscopy (cryo-EM) and allied methods that simian tetherin is targeted in a unique way by the induced refolding of the b subunit of AP-2 from an a-helix to a b-hairpin, creating a binding site for the (G/D)DIWK motif in a crevice between the new b-hairpin and Nef
However, when bound to both tetherin and Nef, b2 (peptide 7–18) underwent 40% less HD exchange (30 s) (Figures 4C and S4A). Slower deuteration was also seen in a and s2 residues in SIVsmm Nef binding regions (Figures S4B and S4C), as expected. The finding that protection from amide HD exchange in the b2 N terminus depends on the presence of both SIVsmm Nef and tetherin strongly supports the conclusions drawn from the cryo-EM structure, which shows that the presence of these two molecules together is required for refolding of this region
We used fluorescence polarization (FP) to determine that Alexa488-tetherin tail bound to AP2DmC and SIVsmm Nef with Kd = 2.7 mM ± 0.1 mM (Figures 1C and 1D), while binding to the separate components or to AP2hemi was undetectable. These data indicate that simian tetherin binds to the AP-2 core and SIVsmm Nef in a cooperative and high-affinity ternary complex that requires elements of the full AP-2 tetramer
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: molecular function regulator (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
We show by cryoelectron microscopy (cryo-EM) and allied methods that simian tetherin is targeted in a unique way by the induced refolding of the b subunit of AP-2 from an a-helix to a b-hairpin, creating a binding site for the (G/D)DIWK motif in a crevice between the new b-hairpin and Nef
However, when bound to both tetherin and Nef, b2 (peptide 7–18) underwent 40% less HD exchange (30 s) (Figures 4C and S4A). Slower deuteration was also seen in a and s2 residues in SIVsmm Nef binding regions (Figures S4B and S4C), as expected. The finding that protection from amide HD exchange in the b2 N terminus depends on the presence of both SIVsmm Nef and tetherin strongly supports the conclusions drawn from the cryo-EM structure, which shows that the presence of these two molecules together is required for refolding of this region
We used fluorescence polarization (FP) to determine that Alexa488-tetherin tail bound to AP2DmC and SIVsmm Nef with Kd = 2.7 mM ± 0.1 mM (Figures 1C and 1D), while binding to the separate components or to AP2hemi was undetectable. These data indicate that simian tetherin binds to the AP-2 core and SIVsmm Nef in a cooperative and high-affinity ternary complex that requires elements of the full AP-2 tetramer
Cross-references: PDB:6OWT
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
We show by cryoelectron microscopy (cryo-EM) and allied methods that simian tetherin is targeted in a unique way by the induced refolding of the b subunit of AP-2 from an a-helix to a b-hairpin, creating a binding site for the (G/D)DIWK motif in a crevice between the new b-hairpin and Nef
However, when bound to both tetherin and Nef, b2 (peptide 7–18) underwent 40% less HD exchange (30 s) (Figures 4C and S4A). Slower deuteration was also seen in a and s2 residues in SIVsmm Nef binding regions (Figures S4B and S4C), as expected. The finding that protection from amide HD exchange in the b2 N terminus depends on the presence of both SIVsmm Nef and tetherin strongly supports the conclusions drawn from the cryo-EM structure, which shows that the presence of these two molecules together is required for refolding of this region
We used fluorescence polarization (FP) to determine that Alexa488-tetherin tail bound to AP2DmC and SIVsmm Nef with Kd = 2.7 mM ± 0.1 mM (Figures 1C and 1D), while binding to the separate components or to AP2hemi was undetectable. These data indicate that simian tetherin binds to the AP-2 core and SIVsmm Nef in a cooperative and high-affinity ternary complex that requires elements of the full AP-2 tetramer
Cross-references: PDB:6OWT
Protein: DP02888 (UniProt Q70627)
Region: residues 60	to 71
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops.
Cross-references: PDB:2NEF
Protein: DP02888 (UniProt Q70627)
Region: residues 149	to 180
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops.
Cross-references: PDB:2NEF
Protein: DP02889 (UniProt P03407)
Region: residues 155	to 179
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal flexible loop of Nef that contained the endocytic dileucine motif was partly truncated in the crystallized complex, nonetheless no electron density was observed starting from residues 155 to 179, in line with the assumption of a flexible loop section (Figure 5A).
Cross-references: PDB:3REB
Protein: DP02889 (UniProt P03407)
Region: residues 155	to 181
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Models of x-ray structures and electron density were produced using PyMOL (Schrodinger). The final structure includes Nef-SF2core residues 72–161 and 183–208 for chain A, residues 71–154 and 182–208 for chain C, Hck32 residues 83–246 for chain B, and residues 83–176 and 182–246 for chain D.
Cross-references: PDB:4U5W
Protein: DP02889 (UniProt P03407)
Region: residues 157	to 179
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In this study we determined a structural conformation of the dileucine-based sorting motif in the C-terminal flexible loop of Nef.
Cross-references: PDB:3RBB
Protein: DP02889 (UniProt P03407)
Region: residues 157	to 179
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the crystal structure, two Nef–HckSH3-B6 complexes form symmetrical contacts by mutual interactions of the 33 residues encompassing C-terminal flexible loop with the core domain structure of the opposing Nef molecule (Figure 3A). These contacts are mediated by residues V152-P154, followed by E164, N165 and S167-D179 as well as V184 of the loop region. They interact with residues in the range of F94 to T121 of the Nef core domain, completed by V70-R75 of the PxxP loop and V186 of the terminal β-strand β5.
Cross-references: PDB:3RBB
Protein: DP02889 (UniProt P03407)
Region: residues 157	to 179
Annotation: endocytosis involved in viral entry into host cell (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In this study we determined a structural conformation of the dileucine-based sorting motif in the C-terminal flexible loop of Nef. The Nef protein of primate lentiviruses HIV and SIV is the only non-transmembrane protein known to traffic via a dileucine motif 36. This endocytic sorting signal is required for the stimulated internalization of T-cell receptor molecules from the surface of an infected cell by Nef and a key factor for the pathogenicity of HIV.
Cross-references: PDB:3RBB
Protein: DP02889 (UniProt P03407)
Region: residues 157	to 179
Annotation: self-assembly (Disorder function)
Evidence: crystallography evidence used in manual assertion
Supporting statements:
In the crystal structure, two Nef–HckSH3-B6 complexes form symmetrical contacts by mutual interactions of the 33 residues encompassing C-terminal flexible loop with the core domain structure of the opposing Nef molecule (Figure 3A). These contacts are mediated by residues V152-P154, followed by E164, N165 and S167-D179 as well as V184 of the loop region. They interact with residues in the range of F94 to T121 of the Nef core domain, completed by V70-R75 of the PxxP loop and V186 of the terminal β-strand β5.
Cross-references: PDB:3RBB
Protein: DP02889 (UniProt P03407)
Region: residues 154	to 180
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density for the flexible central loop (150–176) was not observed, consistent with the disordered nature of this region in the absence of a binding partner.
The flexible central loop corresponds to 154-180 region of the Nef protein according to the PDB.
Cross-references: PDB:6B72
Protein: DP02890 (UniProt Q7K5N4)
Region: residues 195	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered region inside the crossover-loop of Calypso.
Cross-references: PDB:6CGA
Protein: DP02890 (UniProt Q7K5N4)
Region: residues 304	to 334
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered region corresponding to an insertion of 41 aa in the ULD domain of Calypso.
Cross-references: PDB:6CGA
Protein: DP02891 (UniProt Q9V727)
Region: residues 310	to 340
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It is possible that in situ proteolysis used during crystal growth may have removed residues 310–340 of the ASX Deubad, or that the remaining residues of the ASX Deubad adopt alternate conformations in the crystal. Either scenario would suggest a degree of conformational flexibility in the C-terminal region of ASX Deubad.
Cross-references: PDB:6CGA
Protein: DP02891 (UniProt Q9V727)
Region: residues 254	to 273
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region inside the ASX Deubad domain, invisible in the crystal structure.
Cross-references: PDB:6CGA
Protein: DP02892 (UniProt Q3UND0)
Region: residues 65	to 105
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker region between the DM and PH domains (residues 65–109) is disordered.
Flexible linker connecting the homodimerization (DM) and PH domain of Skap2.
Cross-references: PDB:2OTX
Protein: DP02892 (UniProt Q3UND0)
Region: residues 65	to 105
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The linker region between the DM and PH domains (residues 65–109) is disordered.
Flexible linker connecting the homodimerization (DM) and PH domain of Skap2.
Cross-references: PDB:2OTX
Protein: DP02894 (UniProt Q9BZZ5-2)
Region: residues 322	to 335
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 277–278, 322–335, 365–366, 430–431, and 447–454, as well as the four extra N-terminal residues (Gly-Ser-His-Met), artificially added by cloning into pET-28b, were disordered in the crystal.
Cross-references: PDB:3U0R
Protein: DP02894 (UniProt Q9BZZ5-2)
Region: residues 455	to 504
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 API5 (residues 455–504), which contains a nuclear localization signal (Fig. 2) between residues 454–475 and is predicted to be disordered by IUPRED (33), was readily removed by trypsin.
Cross-references: PDB:3U0R
Protein: DP02894 (UniProt Q9BZZ5-2)
Region: residues 455	to 504
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The C-terminal region of API5 (residues 455–504), which contains a nuclear localization signal (Fig. 2) between residues 454–475 and is predicted to be disordered by IUPRED (33), was readily removed by trypsin.
Cross-references: PDB:3U0R
Protein: DP02894 (UniProt Q9BZZ5-2)
Region: residues 455	to 475
Annotation: localization (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The C-terminal region of API5 (residues 455–504), which contains a nuclear localization signal (Fig. 2) between residues 454–475 and is predicted to be disordered by IUPRED (33), was readily removed by trypsin.
Cross-references: PDB:3U0R
Protein: DP02895 (UniProt Q96E14)
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:
Electron density defining the N-terminus of RMI2 was missing, which could indicate that this region of the domain is structurally dynamic.
Cross-references: PDB:3MXN
Protein: DP02896 (UniProt Q91VS8)
Region: residues 869	to 906
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ~70-residue PH1-PH2 linker is disordered except for the 864–868 and the 907–931 segments.
Flexible linker connecting PH1 and PH2 domain corresponds to region 869-906 of the amino acid sequence.
Cross-references: PDB:4GZU
Protein: DP02896 (UniProt Q91VS8)
Region: residues 869	to 906
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The ~70-residue PH1-PH2 linker is disordered except for the 864–868 and the 907–931 segments.
Flexible linker connecting PH1 and PH2 domain corresponds to region 869-906 of the amino acid sequence.
Cross-references: PDB:4GZU
Protein: DP02897 (UniProt Q90VU7)
Region: residues 27	to 56
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Much of the Nef N- and C-terminal loops (residues 27–56 and 162–174, respectively) are disordered and not seen in the structure
Cross-references: PDB:4EMZ
PDB:4EN2
Protein: DP02897 (UniProt Q90VU7)
Region: residues 162	to 174
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Much of the Nef N- and C-terminal loops (residues 27–56 and 162–174, respectively) are disordered and not seen in the structure
Cross-references: PDB:4EMZ
PDB:4EN2
Protein: DP02897 (UniProt Q90VU7)
Region: residues 158	to 168
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The Nef LL motif is well-defined in density and engages the γ-σ1 (Figure 2C) in trans with respect to the μ1 interaction. The Nef sequences 149–157 and 168–179 are disordered over gaps of 22 and 25 Å, respectively between the LL motif and the Nef core
Fig 2 legend. (C) The ExxxLL motif of Nef binds to AP-1σ1 (D) These binding regions of Nef are found on the unstructured loops L1 and L4 but are stabilized in the trimeric assembly
Cross-references: PDB:6D83
PDB:6CM9
Protein: DP02897 (UniProt Q90VU7)
Region: residues 160	to 165
Annotation: protein trimerization (Biological process)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The Nef LL motif is well-defined in density and engages the γ-σ1 (Figure 2C) in trans with respect to the μ1 interaction. The Nef sequences 149–157 and 168–179 are disordered over gaps of 22 and 25 Å, respectively between the LL motif and the Nef core
Fig 2 legend. (C) The ExxxLL motif of Nef binds to AP-1σ1 (D) These binding regions of Nef are found on the unstructured loops L1 and L4 but are stabilized in the trimeric assembly
Cross-references: PDB:6D83
PDB:6CM9
Protein: DP02897 (UniProt Q90VU7)
Region: residues 168	to 179
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The Nef sequences 149–157 and 168–179 are disordered over gaps of 22 and 25 Å, respectively between the LL motif and the Nef core.
Cross-references: PDB:6CM9
PDB:6D83
EMDB:EMD-7453
EMDB:EMD-7457
Protein: DP02898 (UniProt P35585)
Region: residues 219	to 231
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
By combining information about the sequence at the μ2 cleavage site (31) with knowledge of the μ2 structure, we can identify the protease-sensitive segment as a disordered loop around residue 224 (not, as one might have expected, the interdomain linker). The same loop is present and disordered in μ1
The disordered region corresponds to residues 219-231
Cross-references: PDB:1W63
Protein: DP02898 (UniProt P35585)
Region: residues 218	to 231
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
An unstructured region of μ1 (residues 218–231) becomes ordered to interact with both Nef and the MHC-I CD [...] Residues 215–233 of μ1 rearrange from a disordered loop in the crystal structure of the AP1 core into a helix-turn motif when in complex with the MHC-I CD and Nef. 
The region becomes ordered upon binding to MHC-I
Cross-references: PDB:4EMZ
PDB:4EN2
Protein: DP02898 (UniProt P35585)
Region: residues 218	to 231
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
An unstructured region of μ1 (residues 218–231) becomes ordered to interact with both Nef and the MHC-I CD [...] Residues 215–233 of μ1 rearrange from a disordered loop in the crystal structure of the AP1 core into a helix-turn motif when in complex with the MHC-I CD and Nef. 
The region becomes ordered upon binding to MHC-I
Cross-references: PDB:4EMZ
PDB:4EN2
Protein: DP02898 (UniProt P35585)
Region: residues 218	to 231
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
An unstructured region of μ1 (residues 218–231) becomes ordered to interact with both Nef and the MHC-I CD [...] Residues 215–233 of μ1 rearrange from a disordered loop in the crystal structure of the AP1 core into a helix-turn motif when in complex with the MHC-I CD and Nef. 
The region becomes ordered upon binding to MHC-I
Cross-references: PDB:4EMZ
PDB:4EN2
Protein: DP02899 (UniProt P23873)
Region: residues 73	to 88
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first three and last 16 residues of each HipB subunit are disordered and located near a small β-sheet, that is composed of β1 and β1′ (from the other subunit) and forms a “β–lid” (Fig. 2A).
Cross-references: PDB:3HZI
PDB:3DNV
Protein: DP02899 (UniProt P23873)
Region: residues 73	to 88
Annotation: limited proteolysis display site (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
To test the hypothesis that the 16 residue C-terminal stretch is critical for degradation, we cloned a truncated HipB (HipB72) lacking the last 16 residues of HipB into pBR creating pBRhipB72. We measured the rate of in vivo degradation of HipB72 in wild type and Δlon (KLE905 and KLE906, respectively) (Fig. 4). Interestingly, HipB72 is indeed substantially more stabile (t1/2>200 min) than full length HipB in wild type indicating that the unstructured C terminus of HipB is essential for degradation by Lon protease (Fig. 4A). As expected, full length HipB72 is also stable in Δlon background. We purified the truncated HipB (His6-HipB72) and tested it in the Lon in vitro degradation assay. The effect was also noticeable though less pronounced in vitro. The half-life time of HipB changed from 74 min for full length HipB to 130 min in the mutant (Fig. 4B).
Our data show that a disordered C-terminus of HipB serves as a degradation signal for the Lon protease.
Protein: DP02900 (UniProt P0A968)
Region: residues 1	to 74
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Here we report that CspD is subject to proteolysis by the Lon protease both in vivo and in vitro.
To analyse the stability of CspD, in vivo degradation experiments in E. coli MC4100 were performed as described in Experimental procedures . Western blot analysis revealed that CspD indeed is an instable protein (Fig. 2A).
Protein: DP02901 (UniProt J7QA90)
Region: residues 73	to 88
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the repressor complex, AtaR intrinsically disordered region interacts with AtaT at two different sites, folding into different structures, that are involved in two separate functional roles, toxin neutralization and placing the DNA-binding domains of AtaR in a binding-compatible orientation. 


The antitoxin AtaR binds and neutralizes AtaT via its intrinsically disordered C-terminal region (IDR), sufficient to counteract the action of AtaT in vivo

The structure of AtaR shows the RHH dimer adopts an elongated conformation (Fig. 2a). The second α-helix of each monomer extends toward the C terminus from V32 to S69 (S73 to M88 are not visible and are presumably disordered)
While the region with missing residues in the PDB 6GTO is from residues 71-88, the authors limit the region to residues 73-88.
Cross-references: PDB:6GTO