LiteFold/DisProt huggingface dataset:
Protein: DP04101 (UniProt Q9H0W8)
Region: residues 12	to 180
Annotation: pre-molten globule (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Here, we have characterized SMG-9, showing that it comprises an N-terminal 180 residue intrinsically disordered region (IDR) followed by a well-folded C-terminal domain.
The N-terminal domain is an intrinsically disordered region (IDR) essential for the maintenance of the structural integrity of the SMG-1:SMG-8:SMG-9 complex.
In addition, fluorescence spectra with an excitation wavelength of 295 nm revealed a significant increase in the fluorescence emission upon denaturation of NT-SMG-912–180 using 6 M guanidinium hydrochloride compared to native conditions (Figure 3B), strongly suggesting the presence of a certain degree of secondary structure quenching the fluorescence of the two tryptophans of NT-SMG-912–180 in the native protein.
Here, we show that SMG-9 comprises an N-terminal domain with the characteristic features of the so-called intrinsically disordered regions (IDRs) and a well-folded C-terminal domain (12).
We have purified a protein comprising the N-terminal domain and several biophysical approaches (gel filtration chromatography, analytical ultracentrifugation, CD, and UV-spectroscopy) have confirmed unambiguously that this region behaves as a compact 20 kDa domain with the paradigmatic characteristics of unstructured domains as well as a limited presence of secondary structure.
Furthermore, the combination of NMR data and the spectroscopy studies suggests that the conformation of the NT-SMG-9 domain most likely fits into the category of intrinsically unstructured proteins termed ‘pre-molten globules’, where a limited degree of secondary structure could be localized.
Protein: DP04101 (UniProt Q9H0W8)
Region: residues 12	to 180
Annotation: pre-molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we have characterized SMG-9, showing that it comprises an N-terminal 180 residue intrinsically disordered region (IDR) followed by a well-folded C-terminal domain.
The N-terminal domain is an intrinsically disordered region (IDR) essential for the maintenance of the structural integrity of the SMG-1:SMG-8:SMG-9 complex.
A 1H 1D spectrum of NT-SMG-912–180 showed two groups of signals, a first group of thin, well-resolved peaks (6.5–8 ppm) and a group of superposed signals accumulating between 8 and 8.5 ppm (Figure 4A). This spectrum would be compatible with an unfolded polypeptide, being the first group of sharp peaks those signals corresponding to the flexible lateral side chains and the aromatic protons whereas the N–H backbone would appear as those signals between 8 and 8.5 ppm. We also performed 1H-15N-HSQC 2D experiments after labelling NT-SMG-912–180 with 15N (Figure 4B), and we found that the majority of the signals attributable to the N-H backbone overlapped within a very narrow 1H chemical shift, ranging from 7.75 to 8.5 ppm. This is a typical spectrum for intrinsically disordered regions, where defined signals (in contrast to aggregated protein) are concentrated in a narrow range (in contrast to folded proteins). Signals of the two tryptophans present in NT-SMG-912–180 were detected at 10.25, 128.89 ppm and 10.1, 127.48 ppm, 1H, 15N chemical shifts, respectively. These chemical shifts are characteristic of solvent exposed tryptophan residues as the amino acids of a disordered protein. In addition, the HSQC spectrum showed several well-dispersed peaks typical of a folded structure, suggesting the presence of some residual structure as previously suggested by CD and fluorescence spectroscopy data.
1H-15N HSQC spectrum of 15N-labelled NT-SMG-912–180 unambiguously identified this domain as inherently unstructured due to the absence of well dispersed cross peaks.
Here, we show that SMG-9 comprises an N-terminal domain with the characteristic features of the so-called intrinsically disordered regions (IDRs) and a well-folded C-terminal domain (12).
The results obtained by NMR spectroscopy represent the formal proof that the N-terminus of SMG-9 is an IDR.
Furthermore, the combination of NMR data and the spectroscopy studies suggests that the conformation of the NT-SMG-9 domain most likely fits into the category of intrinsically unstructured proteins termed ‘pre-molten globules’, where a limited degree of secondary structure could be localized.
Protein: DP04101 (UniProt Q9H0W8)
Region: residues 2	to 180
Annotation: protein binding (Molecular function)
Evidence: co-purification evidence used in manual assertion
Supporting statements:
Both domains are required for SMG-1 binding and the integrity of the SMG1C complex, whereas the C-terminus is sufficient to interact with SMG-8.
The N-terminal domain is an intrinsically disordered region (IDR) essential for the maintenance of the structural integrity of the SMG-1:SMG-8:SMG-9 complex.
Whereas each product was adequately expressed, only full-length SMG-9 co-purified with SMG-1 and SMG-8 in presence of RNaseA. These experiments indicated that both the N- and C-terminal domains of SMG-9 are necessary for the integrity of the SMG1C complex.
We demonstrate that both the N-terminal IDR and the C-terminal domain of SMG-9 are required for the integrity of the SMG1C complex. Both domains are implicated in SMG-1 binding, since removal of either domain disrupts, totally or partially, the interaction of SMG-9 with SMG-1.
The N-terminal disordered domain of SMG-9 participates in the recognition of SMG-1, and it would be the characteristic malleability of IDRs an adequate structural property to allow the transit of SMG-9 through these distinct macromolecular complexes.
Protein: DP04101 (UniProt Q9H0W8)
Region: residues 2	to 180
Annotation: negative regulation of apoptotic process (Biological process)
Evidence: cell transfection experiment evidence used in manual assertion
Supporting statements:
Accordingly, we found that interfering with SMG-9 by expressing NT-SMG-9 and CT-SMG-9 truncated products, affected the normal response of cells to genotoxic stress and increased susceptibility to apoptosis (Supplementary Figure S4 and Supplementary Data), in agreement with the role described for these complexes in genome stability and apoptosis (3,13).
Cis-platin treatment led to a dose-dependent increase in cell apoptosis that was of higher extent in cells over-expressing the N-terminal or C-terminal domains of SMG-9 than in cells expressing the full length protein or than in mock cells.
Thus, SMG-1 has been shown to participate in the cellular stress response (14,16–18), and we find that the expression of truncated versions of SMG-9 increased the susceptibility to apoptosis (Supplementary Figure S4).
Protein: DP04102 (UniProt P17993)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the final model, the N-terminal 17 residues and residues 181–189 could not be traced because of insufficient electron density.
Residues 1-15 are missing in the structure and are presumably disordered.
Cross-references: PDB:4KDC
Protein: DP04103 (UniProt P0AC51)
Region: residues 153	to 171
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Figure 1 shows the final model which includes amino acid residues 5–152 of four protein monomer chains (designated chains A, B, C, D), eight zinc ions, and two 31 bp strands of DNA (designated chains Y and Z) in the asymmetric unit.
However, we cannot rule out the potential for the disordered C-terminal tail of EcZur to bind a third zinc ion thus leaving any role for this site in EcZur as an open question.
Cross-references: PDB:4MTD
PDB:4MTE
Protein: DP04104 (UniProt Q9NRA2)
Region: residues 1	to 31
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are three patches of residues unresolved in Sialin: N-terminal residues 1 to 31, long luminal loop (L2) between TM1 and TM2 containing residues 69 to 101, and C-terminal residues 489 to 496, because of their poor experimental densities.
Cross-references: PDB:8DWI
EMDB:27755
Protein: DP04104 (UniProt Q9NRA2)
Region: residues 69	to 101
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are three patches of residues unresolved in Sialin: N-terminal residues 1 to 31, long luminal loop (L2) between TM1 and TM2 containing residues 69 to 101, and C-terminal residues 489 to 496, because of their poor experimental densities.
Cross-references: PDB:8DWI
EMDB:27755
Protein: DP04104 (UniProt Q9NRA2)
Region: residues 69	to 101
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are three patches of residues unresolved in Sialin: N-terminal residues 1 to 31, long luminal loop (L2) between TM1 and TM2 containing residues 69 to 101, and C-terminal residues 489 to 496, because of their poor experimental densities.
Cross-references: PDB:8DWI
EMDB:27755
Protein: DP04105 (UniProt O43747)
Region: residues 677	to 699
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No model could be built for the N-terminal hinge region, residues 677–699, due to disorder in the electron density, which might account for the relatively high R-factors; the final values for working and test sets are 22.6 and 24.8% at 1.8 Å resolution, respectively.
Cross-references: PDB:1IU1
Protein: DP04107 (UniProt O95470)
Region: residues 62	to 109
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In each subunit the N-terminal regions spanning residues 62–109 and the C-terminal 18 residues (554 to 568) were disordered, corresponding to absence or poor electron density.
Cross-references: PDB:4Q6R
Protein: DP04107 (UniProt O95470)
Region: residues 554	to 568
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In each subunit the N-terminal regions spanning residues 62–109 and the C-terminal 18 residues (554 to 568) were disordered, corresponding to absence or poor electron density.
Cross-references: PDB:4Q6R
Protein: DP04108 (UniProt P52306-2)
Region: residues 61	to 78
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the N-terminal region, 18 residues (aa 61–78) were disordered, and side chains for 66 C-terminal amino acid residues were not assigned owing to the poor electron density. 
Cross-references: PDB:5XGC
Protein: DP04109 (UniProt Q15326)
Region: residues 172	to 195
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB structure shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:4NS5
Protein: DP04110 (UniProt P0A8W0)
Region: residues 1	to 29
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No density was visible for residues 1–30 and 247–263 in chain A or for residues 1–30 and 245–263 in chain B—presumably these were cleaved by proteolysis or disordered.
Residues 1-29 are missing in both chains and are presumably disordered.
Cross-references: PDB:6ON4
Protein: DP04110 (UniProt P0A8W0)
Region: residues 247	to 263
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No density was visible for residues 1–30 and 247–263 in chain A or for residues 1–30 and 245–263 in chain B—presumably these were cleaved by proteolysis or disordered.
Cross-references: PDB:6ON4
Protein: DP04110 (UniProt P0A8W0)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the resolution of this dataset (Supplementary Fig. 10b) does not allow us to accurately locate the N-terminal extensions or confidently define their role in the assembly process, we note that they would be well placed to form protein–protein interactions with the adjacent NanR dimers to stabilize the complex (Fig. 7f).
Residues 1-20 are missing in all structures and are presumably disordered.
Cross-references: PDB:6WFQ
PDB:6WG7
EMDB:21652
EMDB:21661
Protein: DP04110 (UniProt P0A8W0)
Region: residues 249	to 263
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Density for the α10-helix extended further than the crystal structure, allowing additional residues of the C-terminus in both monomers to be modeled.
Residues 249-263 are missing in all structures and are presumably disordered.
Cross-references: PDB:6WG7
PDB:6WFQ
EMDB:21652
EMDB:21661
Protein: DP04110 (UniProt P0A8W0)
Region: residues 1	to 29
Annotation: positive regulation of protein-containing complex assembly (Biological process)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions.
Here we report that three NanR dimers cooperatively bind to the (GGTATA)3-repeat operator and that cooperativity is mediated by a 32-residue N-terminal extension.
A comparative sequence analysis of homologous proteins (Supplementary Fig. 2) revealed that NanR has a 32-residue N-terminal extension within the DNA-binding domain. To test whether this extension plays a role in cooperativity, we generated a truncated NanR construct (NanR33–263) and determined the effect of this truncation on (GGTATA)3-repeat binding using analytical ultracentrifugation. Whereas for wild-type NanR, several species were evident at 7–9 S (Fig. 2d, blue traces, and Supplementary Table 3), for NanR33–263 at the same concentrations only a single smaller species was evident at 4–5.5 S (Fig. 2d, red traces), demonstrating that although NanR33–263 can bind DNA, it is unable to form the higher-order hetero-complexes. Together, these data implicate the N-terminal extension as a crucial determinant of cooperative assembly.
Collectively, our data show that NanR binds the (GGTATA)3-repeat operator with nanomolar affinity and that binding is cooperative, which is mediated by a unique N-terminal extension.
We defined the region of NanR that is responsible for cooperative binding to within the 32-residue N-terminal extension of the DNA-binding domain, as removal of this extension abolished assembly of the higher-order oligomers.
To repress gene expression, dimers of NanR cooperatively and with nanomolar affinity bind to each of the three GGTATA repeats to form a NanR-dimer3/DNA hetero-complex through rearrangement of their N-terminal DNA-binding domains. This cooperative assembly is believed to be mediated by an N-terminal extension, unique to NanR among closely related GntR-type regulators.
Protein: DP04111 (UniProt Q96C36)
Region: residues 274	to 300
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows that the protein lacks electronic density in this region in the 5 generated monomers, indicating that it is disordered.
Cross-references: PDB:6LHM
Protein: DP04112 (UniProt Q3SYG4)
Region: residues 219	to 232
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Exceptions to this include the protein termini, as residues 1–2 and 370–407 are disordered, as well as several loop regions, where residues 113–117, 219–232, and 254–255 could not be built with confidence.
Cross-references: PDB:4YD8
Protein: DP04112 (UniProt Q3SYG4)
Region: residues 370	to 407
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Exceptions to this include the protein termini, as residues 1–2 and 370–407 are disordered, as well as several loop regions, where residues 113–117, 219–232, and 254–255 could not be built with confidence.
Cross-references: PDB:4YD8
Protein: DP04112 (UniProt Q3SYG4)
Region: residues 210	to 232
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04112 (UniProt Q3SYG4)
Region: residues 801	to 887
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04113 (UniProt Q8NFJ9)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04114 (UniProt A0A0C4DGY3)
Region: residues 78	to 180
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04115 (UniProt Q96RK4)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04115 (UniProt Q96RK4)
Region: residues 424	to 519
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04116 (UniProt A8MTZ0)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04116 (UniProt A8MTZ0)
Region: residues 81	to 92
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Besides BBS5 that was only sub-stoichiometrically bound (Figure 1—figure supplement 1A), all domains were well resolved with only some connecting loops and N-and C-terminal regions missing (Figure 1A, Figure 1—figure supplements 1 and 2).
The electron microscopy of the human BBSome core complex shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:6XT9
EMDB:10617
Protein: DP04117 (UniProt Q8N3I7)
Region: residues 135	to 148
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The parts of the primary structure that could be assigned in the density is shown in full colors, while non-modeled regions are represented in opaque colors.
Cross-references: PDB:6XTB
EMDB:10618
Protein: DP04117 (UniProt Q8N3I7)
Region: residues 254	to 341
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The parts of the primary structure that could be assigned in the density is shown in full colors, while non-modeled regions are represented in opaque colors.
Cross-references: PDB:6XTB
EMDB:10618
Protein: DP04118 (UniProt O43665)
Region: residues 98	to 116
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In our RGS10 solution structure (PDB ID 2I59), the region Leu-90 to Glu-108 (Fig. S4A) shows high flexibility as reflected by low 15N-1H nuclear Overhauser effect (NOE) values (0.5–0.6) and a reduced T1/T2 ratio compared with well ordered parts of the structure (data not shown).
Authors are referring to the 98-116 region of the UniProt sequence.
Cross-references: PDB:2I59