LiteFold/DisProt huggingface dataset:
Protein: DP02569 (UniProt Q8R1S4)
Region: residues 155	to 168
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structure of MIM’s IMD, only one turn of this α-helix is observed for chain A, whereas the helix is fully missing in chain B, possibly due to local disorder in the structure
The crystal structure of the IMD of MIM (N-terminal 250 amino acids) was determined to 1.85 Å resolution, using the single anomalous dispersion method and X-ray data collected from a Se-Met-substituted crystal (Experimental Procedures and Table 1). The IMD forms a dimer (Figure 1B). The structure is well defined in the electron density map, except for three areas, which are disordered: the last six amino acids of chain A, the last eight amino acids of chain B, and amino acids Asp 155 to Ser 168 of chain B.
Cross-references: PDB:2D1L
Protein: DP02570 (UniProt Q8BPB0)
Region: residues 11	to 23
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The overall structure adopts a globular shape comprising the MOB core domain made of nine α-helices (H1-H9) with the N-terminal extension, which forms a β-strand (the SN strand, residues 5-9) at the N-terminal segment of FLFGSRSS (residues 3-10) and a newly formed 4-turn α-helix (residues 24-38, hereafter referred to as the Switch helix), whereas the 10-residue linker between the SN strand and the Switch helix were poorly defined on the current map. Notably, the SN strand forms a β-sheet with the S2 strand (residues 95-98)
Cross-references: PDB:5B6B
PDB:5B5W
PDB:5B5V
Protein: DP02570 (UniProt Q8BPB0)
Region: residues 11	to 23
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The overall structure adopts a globular shape comprising the MOB core domain made of nine α-helices (H1-H9) with the N-terminal extension, which forms a β-strand (the SN strand, residues 5-9) at the N-terminal segment of FLFGSRSS (residues 3-10) and a newly formed 4-turn α-helix (residues 24-38, hereafter referred to as the Switch helix), whereas the 10-residue linker between the SN strand and the Switch helix were poorly defined on the current map. Notably, the SN strand forms a β-sheet with the S2 strand (residues 95-98)
In the autoinhibited form of MOB1, the N-terminal extension forms the very N-terminal β-strand, the SN strand (residues 5-9), forming a β-sheet with the S2 strand, followed by a conformationally flexible linker and the Switch helix bound to the LATS1-binding site. The flexible linker runs along the LATS1-binding surface with electrostatic interactions. Thr12 is located at the conformationally flexible linker and Thr35 is located at the Switch helix.
Cross-references: PDB:5B6B
PDB:5B5W
PDB:5B5V
Protein: DP02571 (UniProt P80192)
Region: residues 298	to 310
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This DFG-in structure had no density in the loop between strand β and helix αC (chain segment 174−180) in the C-terminal domain and in part of the activation loop (294−319) chain segment 296−309.
Cross-references: PDB:3DTC
Protein: DP02571 (UniProt P80192)
Region: residues 298	to 310
Annotation: molecular function activator activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This DFG-in structure had no density in the loop between strand β and helix αC (chain segment 174−180) in the C-terminal domain and in part of the activation loop (294−319) chain segment 296−309.
Cross-references: PDB:3DTC
Protein: DP02571 (UniProt P80192)
Region: residues 173	to 183
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region in PDB:3DTC.
Cross-references: PDB:3DTC
Protein: DP02572 (UniProt P55042)
Region: residues 116	to 125
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Second, the subtle but important switch I conformational switch that reads out the bound GTP in Ras is completely missing in the RGK proteins as they are not observed in the electron density in both Rad and Rem2
Specifically, switch I is disordered in both nucleotide states for both Rad and Rem2, without any detectable interactions between protein and nucleotide.
Cross-references: PDB:3Q72
PDB:3Q7P
PDB:3Q7Q
Protein: DP02572 (UniProt P55042)
Region: residues 149	to 160
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For the RGK proteins, in the Rad:GDP crystal structure and particularly in the Rad:GNP crystal structure, switch II is largely characterized by static disorder.
Cross-references: PDB:3Q72
PDB:3Q7P
PDB:3Q7Q
Protein: DP02573 (UniProt Q8VEL9)
Region: residues 140	to 151
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Specifically, switch I is disordered in both nucleotide states for both Rad and Rem2, without any detectable interactions between protein and nucleotide.
Second, the subtle but important switch I conformational switch that reads out the bound GTP in Ras is completely missing in the RGK proteins as they are not observed in the electron density in both Rad and Rem2
Cross-references: PDB:3Q85
Protein: DP02574 (UniProt P39905)
Region: residues 78	to 117
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-­terminal region (residues 1–39 in chain B and 1–31 in chain D) of GDNF was dis­ordered.
Cross-references: PDB:3FUB
Protein: DP02575 (UniProt P83755)
Region: residues 335	to 344
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
But the carboxy (C) terminus of PsbA (amino acids 335–344), important for the binding of the manganese cluster, appears to be disordered, as there is no density present in that region.
Cross-references: PDB:5MDX
EMDB:EMD-3491
Protein: DP02575 (UniProt P83755)
Region: residues 335	to 344
Annotation: metal ion binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
But the carboxy (C) terminus of PsbA (amino acids 335–344), important for the binding of the manganese cluster, appears to be disordered, as there is no density present in that region.
Cross-references: PDB:5MDX
EMDB:EMD-3491
Protein: DP02576 (UniProt P56777)
Region: residues 480	to 508
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the cryo-EM density map all the transmembrane helices of PsbA, PsbB, PsbC and PsbD are clearly visible and well defined. Whereas the helices are clearly visible, the termini are more difficult to assign.
Cross-references: EMDB:EMD-3491
PDB:5MDX
Protein: DP02577 (UniProt P23321)
Region: residues 240	to 281
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For the extrinsic subunits the density for PsbO has been assigned. The β-barrel is well organized, but for the loops not all densities are resolved.
Cross-references: EMDB:EMD-3491
PDB:5MDX
Protein: DP02578 (UniProt Q16647)
Region: residues 319	to 330
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 320–327 of chain A or residues 319–330 of chain B, and these regions were omitted from the model.
Cross-references: PDB:2IAG
Protein: DP02579 (UniProt Q8VDQ1)
Region: residues 254	to 265
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for residues 254–265.
The present structure does not contain a bound nucleotide, which is most likely the reason for the observed disorder in one of the nucleotide‐recognition loops (residues 254–265).
The Tyr64 side‐chain is disordered in the 18204011 structure, which is most likely due to lack of any bound NADPH.
No electron density was observed for residues 254–265, the side‐chain atoms of D32, Y64, E115, E191, N212, R286, E297, K320, E347, or the rest of the expression and purification tag.
Cross-references: PDB:1VJ1
Protein: DP02579 (UniProt Q8VDQ1)
Region: residues 254	to 265
Annotation: molecular function regulator (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for residues 254–265.
The present structure does not contain a bound nucleotide, which is most likely the reason for the observed disorder in one of the nucleotide‐recognition loops (residues 254–265).
The disordered loop between residues Cys253 and Pro266 comprises a conserved GxxS motif, which stabilizes both the adenine and nicotinamide moieties of the cofactor in the NADPH‐bound form of quinone oxidoreductase.
Cross-references: PDB:1VJ1
Protein: DP02580 (UniProt P28827)
Region: residues 589	to 742
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density for the fourth FN domain, although sufficient to indicate its approximate position, remained largely disordered throughout refinement; therefore, this domain was not included in the final model (fig. S2, A and B).
Cross-references: PDB:2V5Y
Protein: DP02583 (UniProt F1RAX4)
Region: residues 575	to 597
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two C-terminal CaM-binding helices (CaMBP1 and CaMBP2) follow, linked by a disordered segment (Fig. 1, D and E).
The disordered CaMBP1-CaMBP2 linker is conserved in sequence for its central and acidic motif, EEGIQLV in zebrafish STRA6, with the Glu-Gly segment invariant across STRA6 orthologs
CaMBP1 and CaMBP2 are connected by a linker, that is disordered in the structure and that contains a conserved sequence motif (EEGIQLV; fig. S7) similar to the box2 motif of cytokine receptors, which is known to mediate recruitment of JAK family members through their FERM and SH2 domains
Cross-references: PDB:5SY1
PDB:5K8Q
Protein: DP02583 (UniProt F1RAX4)
Region: residues 575	to 597
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Two C-terminal CaM-binding helices (CaMBP1 and CaMBP2) follow, linked by a disordered segment (Fig. 1, D and E).
The disordered CaMBP1-CaMBP2 linker is conserved in sequence for its central and acidic motif, EEGIQLV in zebrafish STRA6, with the Glu-Gly segment invariant across STRA6 orthologs
CaMBP1 and CaMBP2 are connected by a linker, that is disordered in the structure and that contains a conserved sequence motif (EEGIQLV; fig. S7) similar to the box2 motif of cytokine receptors, which is known to mediate recruitment of JAK family members through their FERM and SH2 domains
Cross-references: PDB:5SY1
PDB:5K8Q
Protein: DP02583 (UniProt F1RAX4)
Region: residues 585	to 591
Annotation: molecular adaptor activity (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
CaMBP1 and CaMBP2 are connected by a linker, that is disordered in the structure and that contains a conserved sequence motif (EEGIQLV; fig. S7) similar to the box2 motif of cytokine receptors, which is known to mediate recruitment of JAK family members through their FERM and SH2 domains
Cross-references: PDB:5SY1
PDB:5K8Q
Protein: DP02584 (UniProt F1QGH7)
Region: residues 1	to 126
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 observed for the two terminal domains except for the helix C in the C-terminal domain and an additional α helix flanking the N terminus of armadillo repeat 1.
The final crystal structure obtained from full-length zebrafish β-catenin protein crystals contains residues 126–681
Our crystal structures demonstrate that the N- and C-terminal domains of β-catenin are structurally flexible and clearly do not interact with the armadillo repeat domain with a static conformation.
In our crystal structures, the N- and the C-terminal tails are disordered despite the presence of intact β-catenin R1C and full-length β-catenin in respective crystals. Therefore, we conclude that the N- and C-terminal tails do not interact with the armadillo repeat domain with a specific conformation.
Cross-references: PDB:2Z6G
Protein: DP02584 (UniProt F1QGH7)
Region: residues 680	to 780
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 observed for the two terminal domains except for the helix C in the C-terminal domain and an additional α helix flanking the N terminus of armadillo repeat 1.
The final crystal structure obtained from full-length zebrafish β-catenin protein crystals contains residues 126–681
Our crystal structures demonstrate that the N- and C-terminal domains of β-catenin are structurally flexible and clearly do not interact with the armadillo repeat domain with a static conformation.
In our crystal structures, the N- and the C-terminal tails are disordered despite the presence of intact β-catenin R1C and full-length β-catenin in respective crystals. Therefore, we conclude that the N- and C-terminal tails do not interact with the armadillo repeat domain with a specific conformation.
Cross-references: PDB:2Z6G
Protein: DP02585 (UniProt Q9H900)
Region: residues 253	to 263
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Domain 1 is connected to domain 2 (residues 264–505) through a flexible connector (residues 253–263) that is invisible in the electron density.
The final model includes residues 1–68, 99–211, 222–252, 264–309, 339–560, and 576–590 as well as five additional residues at the N terminus left after the removal of the tag.
Cross-references: PDB:3IF8
Protein: DP02585 (UniProt Q9H900)
Region: residues 253	to 263
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Domain 1 is connected to domain 2 (residues 264–505) through a flexible connector (residues 253–263) that is invisible in the electron density.
Cross-references: PDB:3IF8
Protein: DP02585 (UniProt Q9H900)
Region: residues 69	to 98
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 1–68, 99–211, 222–252, 264–309, 339–560, and 576–590 as well as five additional residues at the N terminus left after the removal of the tag.
Cross-references: PDB:3IF8
Protein: DP02585 (UniProt Q9H900)
Region: residues 212	to 221
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 1–68, 99–211, 222–252, 264–309, 339–560, and 576–590 as well as five additional residues at the N terminus left after the removal of the tag.
Cross-references: PDB:3IF8
Protein: DP02585 (UniProt Q9H900)
Region: residues 310	to 338
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 1–68, 99–211, 222–252, 264–309, 339–560, and 576–590 as well as five additional residues at the N terminus left after the removal of the tag.
Cross-references: PDB:3IF8
Protein: DP02585 (UniProt Q9H900)
Region: residues 561	to 575
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 1–68, 99–211, 222–252, 264–309, 339–560, and 576–590 as well as five additional residues at the N terminus left after the removal of the tag.
Cross-references: PDB:3IF8
Protein: DP02586 (UniProt P10761)
Region: residues 119	to 131
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density could be observed for FG loop residues Pro 119–Asn 131 in the P21212 map.
Cross-references: PDB:3D4C
PDB:3EF7
PDB:3D4G
PDB:5OSQ
Protein: DP02587 (UniProt Q96PM5)
Region: residues 187	to 215
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure of the Pirh2 CTD consists of a 30-residue disordered loop (residues 187–215) followed by a compact, globular fold that incorporates a single zinc ion with four cysteine thiol groups (residues Cys222, Cys225, Cys240 and Cys243) forming a tetrahedral zinc coordination (Fig. 2c). Residues 198 to 205 within the unstructured region showed some α-helical propensity based on their backbone NMR resonances.
In contrast, the 30 amino-acid linker between the RING and the CTD (~30 residues) gives Pirh2 great flexibility to bring together the ubiquitin-charged E2 enzyme with substrates.
Cross-references: PDB:2K2D
Protein: DP02587 (UniProt Q96PM5)
Region: residues 187	to 215
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure of the Pirh2 CTD consists of a 30-residue disordered loop (residues 187–215) followed by a compact, globular fold that incorporates a single zinc ion with four cysteine thiol groups (residues Cys222, Cys225, Cys240 and Cys243) forming a tetrahedral zinc coordination (Fig. 2c). Residues 198 to 205 within the unstructured region showed some α-helical propensity based on their backbone NMR resonances.
In contrast, the 30 amino-acid linker between the RING and the CTD (~30 residues) gives Pirh2 great flexibility to bring together the ubiquitin-charged E2 enzyme with substrates.
Cross-references: PDB:2K2D
Protein: DP02588 (UniProt P47273)
Region: residues 78	to 99
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In MG027, the loop region (between residue 78 to 99) that connects H4 and H5 is much longer than the corresponding loop in mt‐nusB (between residue 76 to 86) and other nusB proteins (Fig. 3). This loop is mostly exposed in the solvent region and is disordered in MG027 structure.
No density was visible for the first 11 N‐terminal amino acids and part of the loop region that connects α‐helix 4 (H4) and α‐helix 5 (H5)
Cross-references: PDB:1Q8C
Protein: DP02588 (UniProt P47273)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In MG027, the loop region (between residue 78 to 99) that connects H4 and H5 is much longer than the corresponding loop in mt‐nusB (between residue 76 to 86) and other nusB proteins (Fig. 3). This loop is mostly exposed in the solvent region and is disordered in MG027 structure.
No density was visible for the first 11 N‐terminal amino acids and part of the loop region that connects α‐helix 4 (H4) and α‐helix 5 (H5)
Cross-references: PDB:1Q8C
Protein: DP02589 (UniProt Q05080)
Region: residues 276	to 300
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An unstructured carboxy-terminal region follows helix α5 in each monomer and also packs against its dimerization partner.
Cross-references: PDB:4WPE
Protein: DP02590 (UniProt P47523)
Region: residues 37	to 74
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C-terminal fragments (residues 37 to 74 and residues 469 to 556), which were truncated in Protein M TD as compared with Protein M, are likely disordered because the three-dimensional reconstructions of a Fab in complex with Protein M and Protein M TD by using negative-stain electron microscopy are nearly identical
Cross-references: PDB:4NZT
PDB:4NZR
Protein: DP02590 (UniProt P47523)
Region: residues 455	to 468
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 455 to 468 in domain II of Protein M TD were flexible and not modeled.
Cross-references: PDB:4NZT
PDB:4NZR
Protein: DP02590 (UniProt P47523)
Region: residues 37	to 74
Annotation: disorder (Structural state)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
The N- and C-terminal fragments (residues 37 to 74 and residues 469 to 556), which were truncated in Protein M TD as compared with Protein M, are likely disordered because the three-dimensional reconstructions of a Fab in complex with Protein M and Protein M TD by using negative-stain electron microscopy are nearly identical
Protein: DP02590 (UniProt P47523)
Region: residues 469	to 556
Annotation: disorder (Structural state)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
The N- and C-terminal fragments (residues 37 to 74 and residues 469 to 556), which were truncated in Protein M TD as compared with Protein M, are likely disordered because the three-dimensional reconstructions of a Fab in complex with Protein M and Protein M TD by using negative-stain electron microscopy are nearly identical