LiteFold/DisProt huggingface dataset:
Protein: DP02879 (UniProt P59594)
Region: residues 661	to 673
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the structrures of ACE2-free SARS-CoV spike glycoprotein with three RBD in down conformation (PDB:6ACC) and with one RBD in up conformation (PDB:6ACD), and in the SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 1 (PDB:6acg), conformation 2 (PDB:6acj) and conformation 3 (PDB:6ack).
Cross-references: PDB:6ACC
PDB:6ACD
Protein: DP02879 (UniProt P59594)
Region: residues 812	to 831
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the structrures of ACE2-free SARS-CoV spike glycoprotein with three RBD in down conformation (PDB:6ACC) and with one RBD in up conformation (PDB:6ACD), and in the SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 1 (PDB:6acg), conformation 2 (PDB:6acj) and conformation 3 (PDB:6ack).
Cross-references: PDB:6ACC
PDB:6ACD
Protein: DP02879 (UniProt P59594)
Region: residues 1120	to 1196
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the structrures of ACE2-free SARS-CoV spike glycoprotein with three RBD in down conformation (PDB:6ACC) and with one RBD in up conformation (PDB:6ACD), and in the SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 1 (PDB:6acg), conformation 2 (PDB:6acj) and conformation 3 (PDB:6ack).
Cross-references: PDB:6ACC
PDB:6ACD
Protein: DP02879 (UniProt P59594)
Region: residues 661	to 673
Annotation: limited proteolysis display site (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The S1/S2 cleavage site is located in a flexible loop of residues 660–675 that is completely exposed in the prefusion S1-S2 trimer spike. The S2’ cleavage site of the SARS-CoV S glycoprotein is highly conserved among coronaviruses and is completely buried in the prefusion SARS-CoV S glycoprotein
Cross-references: PDB:6ACC
PDB:6ACD
Protein: DP02879 (UniProt P59594)
Region: residues 661	to 673
Annotation: limited proteolysis display site (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The S1/S2 cleavage site is located in a flexible loop of residues 660–675 that is completely exposed in the prefusion S1-S2 trimer spike. The S2’ cleavage site of the SARS-CoV S glycoprotein is highly conserved among coronaviruses and is completely buried in the prefusion SARS-CoV S glycoprotein
Protein: DP02879 (UniProt P59594)
Region: residues 661	to 674
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we report the ectodomain structures of the SARS-CoV surface spike trimer in different conformational states determined by single-particle cryo-electron microscopy. The conformation 1 determined at 4.3 Å resolution is three-fold symmetric and has all the three receptor-binding C-terminal domain 1 (CTD1s) of the S1 subunits in “down” positions. The binding of the “down” CTD1s to the SARS-CoV receptor ACE2 is not possible due to steric clashes, suggesting that the conformation 1 represents a receptor-binding inactive state.
Conformation 1 determined at 4.3 Å resolution corresponds to PDB:5WRG.
Cross-references: PDB:5WRG
Protein: DP02879 (UniProt P59594)
Region: residues 1059	to 1196
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we report the ectodomain structures of the SARS-CoV surface spike trimer in different conformational states determined by single-particle cryo-electron microscopy. The conformation 1 determined at 4.3 Å resolution is three-fold symmetric and has all the three receptor-binding C-terminal domain 1 (CTD1s) of the S1 subunits in “down” positions. The binding of the “down” CTD1s to the SARS-CoV receptor ACE2 is not possible due to steric clashes, suggesting that the conformation 1 represents a receptor-binding inactive state.
Conformation 1 determined at 4.3 Å resolution corresponds to PDB:5WRG.
Cross-references: PDB:5WRG
Protein: DP02879 (UniProt P59594)
Region: residues 810	to 830
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in prefusion structure of SARS-CoV spike glycoprotein, conformation 1 (PDB:5x58) and conformation 2 (PDB:5x5b).
Cross-references: PDB:5X5B
PDB:5X58
Protein: DP02879 (UniProt P59594)
Region: residues 1105	to 1193
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in prefusion structure of SARS-CoV spike glycoprotein, conformation 1 (PDB:5x58) and conformation 2 (PDB:5x5b).
Cross-references: PDB:5X5B
PDB:5X58
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 699	to 709
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An atomic model of the cleaved MERS-CoV S1/S2 trimer was built de novo using the 3.7 Å map, except for the flexible regions of S1 CTD and part of S1 NTD, which were fitted by crystal structures. The final model includes residues 18–1,206, with several small breaks due to the poor densities.
Cross-references: PDB:5X5F
PDB:5X59
PDB:5X5C
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 745	to 756
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An atomic model of the cleaved MERS-CoV S1/S2 trimer was built de novo using the 3.7 Å map, except for the flexible regions of S1 CTD and part of S1 NTD, which were fitted by crystal structures. The final model includes residues 18–1,206, with several small breaks due to the poor densities.
Cross-references: PDB:5X5F
PDB:5X59
PDB:5X5C
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 1207	to 1294
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An atomic model of the cleaved MERS-CoV S1/S2 trimer was built de novo using the 3.7 Å map, except for the flexible regions of S1 CTD and part of S1 NTD, which were fitted by crystal structures. The final model includes residues 18–1,206, with several small breaks due to the poor densities.
Cross-references: PDB:5X5F
PDB:5X59
PDB:5X5C
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 367	to 379
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the crystal structure of MERS-CoV S1 RBD in complex with neutralizing antibody CDC2-C2.
Cross-references: PDB:6C6Z
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 427	to 437
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the crystal structure of MERS-CoV S1 RBD in complex with neutralizing antibody CDC2-C2.
Cross-references: PDB:6C6Z
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 579	to 589
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the crystal structure of MERS-CoV S1 RBD in complex with neutralizing antibody CDC2-C2.
Cross-references: PDB:6C6Z
Protein: DP02880 (UniProt K9N5Q8)
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:
Flexible region in the crystal structure of MERS-CoV S1 RBD in complex with a fully human antibody MCA1.
Cross-references: PDB:5GMQ
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 367	to 380
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the crystal structure of MERS-CoV S1 RBD in complex with neutralizing antibody m336.
Cross-references: PDB:4XAK
Protein: DP02880 (UniProt K9N5Q8)
Region: residues 591	to 601
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible region in the crystal structure of MERS-CoV S1 RBD in complex with neutralizing antibody m336.
Cross-references: PDB:4XAK
Protein: DP02881 (UniProt Q09428)
Region: residues 621	to 676
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker connecting the ABC transporter transmembrane region domain and ABC transporter 1 domain.
Cross-references: PDB:6C3P
PDB:6C3O
Protein: DP02881 (UniProt Q09428)
Region: residues 621	to 676
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Flexible linker connecting the ABC transporter transmembrane region domain and ABC transporter 1 domain.
Protein: DP02882 (UniProt Q6A070)
Region: residues 595	to 620
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No clear electron density was evident for N-terminal residues 332–344, HR A loops residues 361–365, HR F residues 558–562, and the C-terminal residues 595–620.
Cross-references: PDB:5DN7
Protein: DP02883 (UniProt F1QR43)
Region: residues 51	to 72
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model has excellent density for most residues except for the N-terminal flexible loop (Pro50–Val71) and a small internal loop (Asp212–Ser215).
the N-terminal flexible loop at Pro50–Val71 corresponds to Pro51-Val72.
Cross-references: PDB:4PXQ
PDB:4PW2
Protein: DP02884 (UniProt F1RE08)
Region: residues 305	to 316
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density is associated with residues 305–316 of chain A and 155–157, 183–186, 232–243, and 305–316 of chain B, so these regions were omitted from the model.
Cross-references: PDB:3B98
PDB:3B99
Protein: DP02884 (UniProt F1RE08)
Region: residues 232	to 243
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density is associated with residues 305–316 of chain A and 155–157, 183–186, 232–243, and 305–316 of chain B, so these regions were omitted from the model.
Cross-references: PDB:3B98
PDB:3B99
Protein: DP02885 (UniProt Q10589)
Region: residues 79	to 89
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This might be due to flexibility within the region (residues 79 to 89) connecting the N-terminal and coiled-coil domains as documented by the sensitivity to proteolysis and the absence of an ordered structure for residues 80 to 88.
Protein: DP02885 (UniProt Q10589)
Region: residues 79	to 89
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This might be due to flexibility within the region (residues 79 to 89) connecting the N-terminal and coiled-coil domains as documented by the sensitivity to proteolysis and the absence of an ordered structure for residues 80 to 88.
Protein: DP02886 (UniProt Q5QGG3)
Region: residues 184	to 202
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here, we determine the structure of SIVmac239 Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3
The model contains residues 103–233 of SIV Nef and residues 80–134 of the SH3 domain, whereas no electron density was identified for the CD4 peptide (Fig. 1a). 
Residues 66-102 (PDB 5nuh) and 87-106 (5nui) are disordered in all structures, and Residues 184-202 containing the ExxxLL sorting motif (5nui) are disordered in the unbound state
Cross-references: PDB:5NUI
PDB:5NUH
Protein: DP02886 (UniProt Q5QGG3)
Region: residues 66	to 102
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here, we determine the structure of SIVmac239 Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3
The model contains residues 103–233 of SIV Nef and residues 80–134 of the SH3 domain, whereas no electron density was identified for the CD4 peptide (Fig. 1a). 
Residues 66-102 (PDB 5nuh) and 87-106 (5nui) are disordered in all structures, and Residues 184-202 containing the ExxxLL sorting motif (5nui) are disordered in the unbound state
Cross-references: PDB:5NUI
PDB:5NUH
Protein: DP02886 (UniProt Q5QGG3)
Region: residues 87	to 106
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we determine the structure of SIVmac239 Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3
Nef… contains an N-terminal membrane anchor domain of 60–120 amino acids length followed by a core domain of 130–150 amino acids, containing a highly conserved dileucine-based sorting motif at the center of a C-terminal flexible loop27. This exposed sorting motif enables Nef to interact with AP2 and to induce the internalization of its target receptors. 
Residues 66-102 (PDB 5nuh) and 87-106 (5nui) are disordered in all structures, and Residues 184-202 containing the ExxxLL sorting motif (5nui) are disordered in the unbound state [...] At the contact interfaces a three-fold rotational symmetry appears with each C-terminal flexible loop of Nef contacting the sorting motif recognition site of the neighboring Nef–SH3 heterodimer (Fig. 1a). In this crystallographic assembly, the EEHYLM sorting motif of the C-terminal flexible loop interacts with the hydrophobic crevice [...] Again, the sorting motif of one Nef molecule in the asymmetric units contacts the hydrophobic crevice of another Nef molecule (Fig. 1b). In this structure, the electron density map was visible for all residues in the dileucine-based sorting motif, providing detailed molecular insights into the interaction of Nef with endocytic sorting motifs (Fig. 1c). 
The region encompassing the ExxxLL sorting motif (5nui) becomes ordered in the Nef-bound state, emulating its interaction with the AP2 adaptor complex
Cross-references: PDB:5NUI
PDB:5NUH
Protein: DP02886 (UniProt Q5QGG3)
Region: residues 87	to 106
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we determine the structure of SIVmac239 Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3
Nef… contains an N-terminal membrane anchor domain of 60–120 amino acids length followed by a core domain of 130–150 amino acids, containing a highly conserved dileucine-based sorting motif at the center of a C-terminal flexible loop27. This exposed sorting motif enables Nef to interact with AP2 and to induce the internalization of its target receptors. 
Residues 66-102 (PDB 5nuh) and 87-106 (5nui) are disordered in all structures, and Residues 184-202 containing the ExxxLL sorting motif (5nui) are disordered in the unbound state [...] At the contact interfaces a three-fold rotational symmetry appears with each C-terminal flexible loop of Nef contacting the sorting motif recognition site of the neighboring Nef–SH3 heterodimer (Fig. 1a). In this crystallographic assembly, the EEHYLM sorting motif of the C-terminal flexible loop interacts with the hydrophobic crevice [...] Again, the sorting motif of one Nef molecule in the asymmetric units contacts the hydrophobic crevice of another Nef molecule (Fig. 1b). In this structure, the electron density map was visible for all residues in the dileucine-based sorting motif, providing detailed molecular insights into the interaction of Nef with endocytic sorting motifs (Fig. 1c). 
The region encompassing the ExxxLL sorting motif (5nui) becomes ordered in the Nef-bound state, emulating its interaction with the AP2 adaptor complex
Cross-references: PDB:5NUI
PDB:5NUH
Protein: DP02886 (UniProt Q5QGG3)
Region: residues 87	to 106
Annotation: receptor-mediated endocytosis of virus by host cell (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we determine the structure of SIVmac239 Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3
Nef… contains an N-terminal membrane anchor domain of 60–120 amino acids length followed by a core domain of 130–150 amino acids, containing a highly conserved dileucine-based sorting motif at the center of a C-terminal flexible loop27. This exposed sorting motif enables Nef to interact with AP2 and to induce the internalization of its target receptors. 
Again, the sorting motif of one Nef molecule in the asymmetric units contacts the hydrophobic crevice of another Nef molecule (Fig. 1b). In this structure, the electron density map was visible for all residues in the dileucine-based sorting motif, providing detailed molecular insights into the interaction of Nef with endocytic sorting motifs (Fig. 1c). 
We find that Nef is indeed able to act like an adapter by binding to dileucine-based sorting motifs embedded in the plasma membrane while simultaneously exposing its own dileucine motif within the C-terminal flexible loop to the cytosol. This is possible by a dipolar electrostatic surface charge character of Nef. The hydrophobic crevice that interacts with the dileucine motifs is surrounded by positively charged residues, whereas the C-terminal flexible loop with the ExxxLL sorting motif in its center is largely negatively charged. This enables Nef to pick up the cytosolic tail sequences of T cell surface receptors at the plasma membrane and couple them to the endocytic adapter protein machinery. 
Cross-references: PDB:5NUI
PDB:5NUH
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: disorder (Structural state)
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
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: disorder to order (Structural transition)
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
Protein: DP02887 (UniProt P62944)
Region: residues 7	to 18
Annotation: protein binding (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
Cross-references: PDB:6OWT