LiteFold/DisProt huggingface dataset:
Protein: DP02960 (UniProt P00880)
Region: residues 410	to 472
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Fitting of the RbcL8 core from the crystal structure showed that density accommodating the ∼60 C-terminal residues (residues 413–475) of the RbcL subunits was missing in the cryo-EM density map (Fig. 3c, d), indicating that this segment is disordered.
Residues 413 and 475 correspond to residues 410 and 472 (respectively) in the Uniprot and PDB associated sequences.
Protein: DP02960 (UniProt P00880)
Region: residues 410	to 472
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
On RbcX2 binding, the previously ‘free’ C-terminal segment of RbcL seems to be pulled back towards the main body of the subunit and becomes tethered via the interaction of the ultimate C terminus with the central crevice of RbcX2. This RbcX2-mediated ordering of the RbcL C termini may also provide a platform for RbcS docking. 
Residues 413 and 475 correspond to residues 410 and 472 respectively.
Cross-references: PDB:2WVW
Protein: DP02960 (UniProt P00880)
Region: residues 410	to 472
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
On RbcX2 binding, the previously ‘free’ C-terminal segment of RbcL seems to be pulled back towards the main body of the subunit and becomes tethered via the interaction of the ultimate C terminus with the central crevice of RbcX2.
These interactions with RbcX2 may exert a stabilizing effect on the N-terminal domain, as indicated by the partial protease protection of the N-terminal ∼60 residues of RbcL by RbcX2 (data not shown).
Cross-references: PDB:2WVW
Protein: DP02960 (UniProt P00880)
Region: residues 410	to 472
Annotation: protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.
The resulting tentative model for the RbcL8–Raf14 complex (Fig. 5g,h) is consistent with a role of Raf1 in stabilizing RbcL2 and allowing its assembly into the RbcL8 core complex.
 Thus, it seems plausible that the C-terminal residues of RbcL are also ordered in the complex with Raf1
Protein: DP02960 (UniProt P00880)
Region: residues 410	to 472
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
To elucidate how Raf1 mediates Rubisco assembly, we obtained a higher-resolution structure of the Syn7942 RbcL-Raf1 supercomplex expressed in Escherichia coli using cryo-EM (SI Appendix, Fig. S2).
Protein: DP02960 (UniProt P00880)
Region: residues 410	to 472
Annotation: molecular function regulator (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
"This movement could in turn destabilize the interaction of the RbcL C terminus with RbcX2, thus triggering RbcX2 release and final maturation of the Rubisco holoenzyme."
On RbcX2 binding, the previously ‘free’ C-terminal segment of RbcL seems to be pulled back towards the main body of the subunit and becomes tethered via the interaction of the ultimate C terminus with the central crevice of RbcX2. This RbcX2-mediated ordering of the RbcL C termini may also provide a platform for RbcS docking.
Cross-references: PDB:2WVW
Protein: DP02960 (UniProt P00880)
Region: residues 461	to 466
Annotation: protein binding (Molecular function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
Binding of Syn6301-RbcX2(FLAG), AnaCA-RbcX2(FLAG) and Syn7002-RbcX2 to an array of dodecapeptides, with a 10 residue overlap, covering the sequence of the last 40 amino-acids of Syn7002-RbcL, Syn6301-RbcL and Ana7120-RbcL (shown on top)
The consensus motif for RbcX2 binding inferred by this analysis corresponds to residues 461 to 466 (EIKFEF).
Protein: DP02960 (UniProt P00880)
Region: residues 460	to 470
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Isothermal titration calorimetry confirmed that Syn6301-RbcX2 bound the C-terminal sequence of RbcL (KEIKFEFETMD) with low affinity (Kd ∼105 µM) (Supplementary Fig. 3a, b).
Protein: DP02961 (UniProt Q9SR19)
Region: residues 438	to 449
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal 12 residues were disordered in all
crystal lattices.
Cross-references: PDB:4WT4
PDB:4WT5
Protein: DP02961 (UniProt Q9SR19)
Region: residues 270	to 285
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Dmax of the full-length AtRaf1.2 dimer was ∼208 Å, and the radius of gyration (Rg) was 52 Å; we obtained similar values for Syn7942-Raf1. This suggested that the highly charged, flexible linker allows dynamic movements of the Raf1α domains relative to the β-domain dimer, as supported by an ensemble model of the AtRaf1.2 structure (Supplementary Fig. 3e).
The limits of the disordered region were further verified from the structural data on the domain limits and supported by MS analysis.
Protein: DP02962 (UniProt Q9SN68)
Region: residues 32	to 44
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density in the nucleotide-free state and in the VPS9a mutant (D185N) GDP-bound form.
Switch I of ARA7 (residues 32-44) in ARA7-GDP/VPS9a(D185N) is disordered and indicated as transparent green dots. 
Cross-references: PDB:2EFD
PDB:2EFH
Protein: DP02962 (UniProt Q9SN68)
Region: residues 32	to 44
Annotation: molecular sequestering activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Involved in nucleotide binding (GDP) and exchange
Cross-references: PDB:2EFC
PDB:2EFE
Protein: DP02962 (UniProt Q9SN68)
Region: residues 32	to 44
Annotation: small molecule binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Involved in nucleotide binding (GDP) and exchange
Cross-references: PDB:2EFC
PDB:2EFE
Protein: DP02962 (UniProt Q9SN68)
Region: residues 32	to 44
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
After GTP coming into the binary complex of Rab/Vps9 domain, the conformational change is occurred in switch I and II of Rab and Rab is re-orientated to the compacted form. 
Cross-references: PDB:2EFC
PDB:2EFE
PDB:2EFH
PDB:2EFD
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectra showed a strong negative absorbance at 200 nm for His6-HvNAC005(173–355), His6-HvNAC013(177–346), and HvNAC013(177–346) with little ellipticity around 220 nm indicating lack of a significant amount of secondary structure and highly characteristic of unstructured proteins (Figs. 6, A and B, and ​77B).
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
This aspect of HvNAC013(177–346) was analyzed using size exclusion chromatography. The calculated molecular mass of HvNAC013(177–346) is 18.0 kDa, corresponding to a Stokes radius of 20.5 Å for a globular protein. However, HvNAC013(177–346) eluted in a volume corresponding to a molecular mass of 41.5 kDa and a Stokes radius of 28.01 Å (Fig. 6C). This suggested that HvNAC013(177–346) exists in a pre-molten globule-like state (Fig. 6C).
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR experiments using 15N-labeled HvNAC013(177–346) were also performed to examine for both the secondary structure and oligomeric state of HvNAC013(177–346). The HSQC spectrum showed a clustering of signals with low dispersion in the proton dimension (Fig. 6D) suggesting that HvNAC013(177–346) is highly unfolded.
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
A directed yeast two-hybrid assay using full-length HvNAC013 and HvRCD1 as bait and prey, respectively, suggested that the proteins interacted (Fig. 8B). Similar results were obtained when HvRCD1 acted as bait and HvNAC013 as prey (Fig. 8C). Analysis of the ability of the isolated domains of HvNAC013 to interact with HvRCD1 showed that the interaction was mediated by the TRD of HvNAC013 (Fig. 8D). 
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Recombinant versions of the HvNAC013 TRD and HvRCD1 RST domains, His6-HvNAC013(177–346) and GST-HvRCD1(485–579), were produced and used for in vitro pulldown assays (Fig. 8E). Western blot analysis showed that His6-HvNAC013(177–346) bound to immobilized GST-HvRCD1(485–579), but not to GST.
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 250	to 346
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
In contrast to full-length HvNAC013 and its TRD, HvNAC013(1–250), lacking the 96 C-terminal amino acid residues of HvNAC013, did not interact with HvRCD1. In contrast, mutation of the conserved aspartate (D217A) and leucine (L212A) of the LP motif had no effect on the interaction. In conclusion, the ability of the HvNAC013 TRD to interact with RCD1 resides within the 96 C-terminal amino acid residues of HvNAC013, and no interaction was detected between the LP motif
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 250	to 346
Annotation: molecular function regulator (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
HvNAC013 interacted with barley radical-induced cell death 1 (RCD1) via the very C-terminal part of its TRD, outside of the region containing the LP motif. 
In conclusion, the ability of the HvNAC013 TRD to interact with RCD1 resides within the 96 C-terminal amino acid residues of HvNAC013.
The indispensability of the 96 C-terminal amino acid residues of HvNAC013 for the interaction with HvRCD1 together with the predicted structure for the last 24 residues of HvNAC013 (Fig. 4) may suggest that a MoRF is present in this part of HvNAC013 (6, 7).
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: molecular function activator activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Coding regions of HvNAC005 and HvNAC013 were fused to yeast GAL4 DBD (Fig. 5A) and analyzed for their ability to activate transcription and promote yeast growth in the absence of histidine and adenine. Murine tumor suppressor p53 (pVA3-1) and SV40 large antigen (pTD1-1) were included as positive controls for transformation and activity dependent selective growth (38). Full-length HvNAC013 was able to activate transcription, and the activation potential resided in the C terminus (residues 177–346), whereas the N-terminal NAC domain (residues 1–176) was unable to activate reporter genes (Fig. 5C).
HvNAC013 correspond to Hordeum vulgare NAC transcription factor.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: molecular function regulator (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of interacting HvNAC013(177–346) and His6-HvRCD1(485–579) seemed to be dominated by the HvNAC013 structure (Fig. 9D). A change in absorbance at both 222 and 208 nm was observed for mixed compared with individual proteins suggesting a shift toward a more unfolded state or more extended structure within the complex (Fig. 9D). This is a strong indication that HvNAC013 and HvRCD1 do not interact through a coupled binding and folding mechanism, but rather through a slight reorientation of the conformational ensemble of either or both proteins, possibly involving extended structure formation.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of interacting HvNAC013(177–346) and His6-HvRCD1(485–579) seemed to be dominated by the HvNAC013 structure (Fig. 9D). A change in absorbance at both 222 and 208 nm was observed for mixed compared with individual proteins suggesting a shift toward a more unfolded state or more extended structure within the complex (Fig. 9D). This is a strong indication that HvNAC013 and HvRCD1 do not interact through a coupled binding and folding mechanism, but rather through a slight reorientation of the conformational ensemble of either or both proteins, possibly involving extended structure formation.
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Spectra of individual proteins and mixed HvNAC013(177–346) and His6-HvRCD1(485–579) were recorded (Fig. 9, A and B). The sum of the spectra of individual proteins was used as reference for noninteracting proteins. Δλmax was calculated and a minor change of 4.5 and 3.0 nm in fluorescence λmax upon mixing of the two proteins was observed from the excitation wavelengths. This suggested that the environment around the aromatic residues changed to more hydrophobic upon interaction (Fig. 9B).
Protein: DP02965 (UniProt F6IAY2)
Region: residues 177	to 346
Annotation: molecular function regulator (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Spectra of individual proteins and mixed HvNAC013(177–346) and His6-HvRCD1(485–579) were recorded (Fig. 9, A and B). The sum of the spectra of individual proteins was used as reference for noninteracting proteins. Δλmax was calculated and a minor change of 4.5 and 3.0 nm in fluorescence λmax upon mixing of the two proteins was observed from the excitation wavelengths. This suggested that the environment around the aromatic residues changed to more hydrophobic upon interaction (Fig. 9B).
Protein: DP02966 (UniProt Q9SU24)
Region: residues 216	to 234
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The two linker regions on both sides of PHD finger that are connected to the BAH domain (residues 156–161 and 216–234) are disordered and were not built into the final model (Figure 1D).
Cross-references: PDB:5HH7
Protein: DP02966 (UniProt Q9SU24)
Region: residues 216	to 234
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The two linker regions on both sides of PHD finger that are connected to the BAH domain (residues 156–161 and 216–234) are disordered and were not built into the final model (Figure 1D).
Cross-references: PDB:5HH7
Protein: DP02967 (UniProt Q05128)
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:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:7JZT
Protein: DP02967 (UniProt Q05128)
Region: residues 309	to 326
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The core of the linear hexamer consists of four NTDs from which the linked CTDs are disordered or ‘sprung’ and not resolved.
Cross-references: PDB:7JZT
Protein: DP02968 (UniProt Q44177)
Region: residues 115	to 134
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 115 to 134 were not resolved in any of the RbcX peptide chains.
Cross-references: PDB:2PEN
PDB:2PEQ
PDB:2PEI
PDB:2PEM
Protein: DP02968 (UniProt Q44177)
Region: residues 110	to 134
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Indeed, limited proteolysis of RbcX resulted in the removal of the poorly conserved 25 C-terminal residues (Figure S3), leaving a stable core domain of residues 1–109 (RbcX(ΔC25)) which was active in Rubisco assembly (Figure S4).
Protein: DP02969 (UniProt O80837)
Region: residues 1	to 77
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In contrast, AtREM1.3-N showed low ellipticity at 190 nm and a minimum ellipticity at 200 nm, the characteristic pattern of a disordered conformation (57% random coil) (Fig. 1E, table).
Protein: DP02969 (UniProt O80837)
Region: residues 1	to 77
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The abnormally slow migration of AtREM1.3-N supports the presence of intrinsic disorder within this region (32, 33).
Protein: DP02969 (UniProt O80837)
Region: residues 1	to 61
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Incubation of purified AtREM1.3 with increasing concentrations of PK led to the accumulation of a stable fragment migrating at 17 kDa (Fig. 1F). Sequence determination by mass spectrometry of the proteolysis-resistant fragment resulted in the identification of residues 62–176, representing the majority of the C-terminal region.
Protein: DP02969 (UniProt O80837)
Region: residues 177	to 190
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Incubation of purified AtREM1.3 with increasing concentrations of PK led to the accumulation of a stable fragment migrating at 17 kDa (Fig. 1F). Sequence determination by mass spectrometry of the proteolysis-resistant fragment resulted in the identification of residues 62–176, representing the majority of the C-terminal region.
Protein: DP02969 (UniProt O80837)
Region: residues 1	to 77
Annotation: molecular function regulator (Molecular function)
Evidence: GAL4-VP16 functional complementation evidence used in manual assertion
Supporting statements:
For this, different truncated AtREM1.3 variants were co-expressed with AtIMPa1, AtIMPa2, AtIMPa3, and AtIMPa6 using the GAL4 system.
Deletion of the N-terminal region led to a significant reduction in the interaction strength with AtIMPa1 and AtIMpa2 in the quantitative β-galactosidase assay (Fig. 5, B and D), indicating that the ID N-terminal region also contributed to interaction with the importin α proteins.
Protein: DP02969 (UniProt O80837)
Region: residues 64	to 68
Annotation: phosphorylation display site (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Phosphorylation of Ser-66 in the intrinsically disordered N-terminal region decreases the interaction strength with the importin α proteins.
Furthermore, constitutive phosphorylation of Ser-66 decreases the interaction with importin α proteins, implying that phosphorylation of AtREM1.3 in its ID N-terminal domain could be a mechanism of controlling protein interactions with cytosolic proteins.
Phosphoablative (AtREM1.3-S66A) and phosphomimetic (AtREM1.3-S66D) mutant variants of Ser-66 were created and used to assess the possible impact of phosphorylation within the ID N-terminal domain in the interaction with importin α proteins. Quantitative β-galactosidase assays showed a tendency to reduced interaction strength of AtIMpa1 and AtIMpa2 with the phosphomimetic variant.
Protein: DP02969 (UniProt O80837)
Region: residues 64	to 68
Annotation: molecular function regulator (Molecular function)
Evidence: GAL4-VP16 functional complementation evidence used in manual assertion
Supporting statements:
Phosphoablative (AtREM1.3-S66A) and phosphomimetic (AtREM1.3-S66D) mutant variants of Ser-66 were created and used to assess the possible impact of phosphorylation within the ID N-terminal domain in the interaction with importin α proteins. Quantitative β-galactosidase assays showed a tendency to reduced interaction strength of AtIMpa1 and AtIMpa2 with the phosphomimetic variant. Interestingly, this reduction is comparable with the reduction observed in the variant devoid of the N-terminal domain (Fig. 5, B and D).
Protein: DP02971 (UniProt Q5JRX3)
Region: residues 774	to 787
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it's disordered.
Cross-references: PDB:4L3T
Protein: DP02975 (UniProt P06734)
Region: residues 150	to 159
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 160–288 of CD23, 1 calcium ion, and 173 water molecules. The model is missing 13 N-terminal residues, 33 C-terminal residues (289–321), and internal residues 253–257.
Cross-references: PDB:2H2T
Protein: DP02975 (UniProt P06734)
Region: residues 293	to 321
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 30 C-terminal residues (292–321) of the construct is not observed, and these residues are not part of the predicted lectin domain.
Cross-references: PDB:2H2R
PDB:2H2T
Protein: DP02975 (UniProt P06734)
Region: residues 244	to 258
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the absence of Ca2+ binding to CD23, as in the complex presented here, the loop including Asp258 is found to be partially flexible
Cross-references: PDB:5LGK
Protein: DP02976 (UniProt Q05193)
Region: residues 347	to 356
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 63–64, 110–112, 143–149, 347–356, 394–404, 446–447, 500–517, 534–537, 578–581 and 632–652 are disordered. 
α1S in dynamin 1 is subdivided into α1NS, α1MS and α1CS by two disordered loops, L1NS and L1CS, compared to a single break of the corresponding helix in MxA.
Cross-references: PDB:3SNH