protein crystal structures  (Databank Inc)

Journal: Cell

Article Title: The E3-ome gene-centric compendium reveals the human E3 ligase landscape

doi: 10.1016/j.cell.2026.01.029

Figure Lengend Snippet: Resolving RING/PHD domain conflicts, related to (A) The RING/PHD domain family of E3s from Ge et al. (2018) were initially annotated for the presence of PHD and RING using InterPro. Proteins with both RING and PHD domain annotations were analyzed for conflicting annotations on InterPro. Conflict regions were further analyzed by PHD domain curators to identify PHD domains. Proteins with an asterisk ( ∗ ) are high-confidence RING E3s. (B) Multiple sequence alignment showing residues assessed for RING/PHD domain conflicts from PHRF1, TRIM28, UHRF2, BAZ1B, and NSD2 (purple) compared with experimentally solved PHD domains (green and blue). The most similar domains (from AlphaFold and PDB) compared with the queried domains of PHRF1, TRIM28, UHRF2, BAZ1B, and NSD2 are also indicated. Proteins with experimentally solved structures (green and blue) have PDB identifiers indicated. A key β-sheet region of some PHD domains interacting with histones is shown (orange bar). Alignment also shows amino acid positions in which some PHD domains could use a tryptophan (orange circle) or an aspartate (blue circle) to bind histones. An aromatic acid, typically tryptophan, is also usually found in PHD fingers positioned before the last cysteine pair (gold circle). (C) AlphaFold database predicted structures from the RING/PHD conflicting regions of PHRF1, TRIM28, UHRF2, BAZ1B, and NSD2 compared with experimentally solved PHD domains.

Article Snippet: The Tabula Sapiens dataset (version 1 and version 2) was used for single-cell RNA-seq analyses., Experimental and predicted protein structures were obtained from RSCB Protein Data Bank (RSCB PDB), AlphaFold Protein Structure Database (Google DeepMind and EMBL-EBI, https://alphafold.ebi.ac.uk ) and AlphaFold Server (Google DeepMind, https://alphafoldserver.com/ ).,

Techniques: Sequencing

Journal: Cell

Article Title: The E3-ome gene-centric compendium reveals the human E3 ligase landscape

doi: 10.1016/j.cell.2026.01.029

Figure Lengend Snippet: Phylogenetic tree of RING and dRING domains Dendrogram shows the similarity of the RING and dRING domains based on DALI’s all-against-all structure comparison of AlphaFold predicted structures. See also .

Article Snippet: The Tabula Sapiens dataset (version 1 and version 2) was used for single-cell RNA-seq analyses., Experimental and predicted protein structures were obtained from RSCB Protein Data Bank (RSCB PDB), AlphaFold Protein Structure Database (Google DeepMind and EMBL-EBI, https://alphafold.ebi.ac.uk ) and AlphaFold Server (Google DeepMind, https://alphafoldserver.com/ ).,

Techniques: Comparison

Journal: Cell

Article Title: The E3-ome gene-centric compendium reveals the human E3 ligase landscape

doi: 10.1016/j.cell.2026.01.029

Figure Lengend Snippet: Diversity of the SP-RING and U-box protein classes, related to , , and (A) Sequence alignment of 3 prototypical RING domains (CBL, RNF2, RNF8) with SP-RING domains from human and yeast. SP-RING domains typically lack the second, fifth, and sixth zinc-coordinating cysteine residues found in RING domains. (B) Structural comparison of the CBL RING domain (a prototypical example) with experimentally solved and predicted structures of SP-RING domains from yeast and human. The overall fold of the CBL RING domain is conserved in SP-RING domains, except SP-RING domains lack the first zinc coordination site. (C) Structure of the yeast Ubc9-donor SUMO/Siz1-backside SUMO/PCNA complex. Backside SUMO is omitted in this depiction. A detailed view of the SP-RING domain interaction with Ubc9 demonstrates a binding mechanism similar to other RING domains with E2s. This interaction involves residues of the central helix and the hydrophobic residue before the second zinc-coordinating cysteine. (D) Sequence alignment of the CBL RING domain with the U-box of several proteins (guided by evidence from curation, literature annotation, and databases). (E) Experimentally solved structures and AlphaFold database structures of regions in (A) to compare the overall fold conservation of the U-box of different proteins with the RING domain of CBL. Residues annotated across all structures are based on pairwise comparison between the CBL RING domain and a potential U-box of interest to identify zinc-coordinating residues that are absent.

Article Snippet: The Tabula Sapiens dataset (version 1 and version 2) was used for single-cell RNA-seq analyses., Experimental and predicted protein structures were obtained from RSCB Protein Data Bank (RSCB PDB), AlphaFold Protein Structure Database (Google DeepMind and EMBL-EBI, https://alphafold.ebi.ac.uk ) and AlphaFold Server (Google DeepMind, https://alphafoldserver.com/ ).,

Techniques: Sequencing, Comparison, Binding Assay, Residue

Journal: Cell

Article Title: The E3-ome gene-centric compendium reveals the human E3 ligase landscape

doi: 10.1016/j.cell.2026.01.029

Figure Lengend Snippet: Diversity of CRL3 and CRL4, related to (A) Schematic representation of the CRL3 complex, highlighting the substrate receptor (BTB domain-containing protein), Cullin scaffold (CUL3), and catalytic module (RBX1). (B) Sequence alignment of the BTB domain from a subfamily of BTB proteins that possess a BACK domain. Proteins chosen for this alignment have at least 3 high-throughput and 3 low-throughput independent studies showing interaction with CUL3. The 2 structures are shown to highlight key residues of the φ-X-E motif (within the BTB domain) and the 3-box motif (within the BACK domain) from KLHL3 and KLHL11 contributing to interactions with CUL3. The residues of KLHL3 that contact CUL3 (orange circle) are indicated based on findings from. The 3-box motif forms the first 2 helices (paired helix) of the BACK domain. (C) Schematic representation of the CRL4 complex, highlighting the substrate receptor (DDB1-binding protein), the adaptor protein (DDB1), Cullin scaffold (CUL4A/CUL4B), and catalytic module (RBX1). (D) The structure represents a dimeric CRL4 DCAF1 E3 complex. The interchangeable substrate receptor DCAF1 is shown bound to DDB1 through a helix-loop-helix motif. The 3 β-propeller domains of DDB1 are indicated as DDB1 BPA, DDB1 BPB, and DDB1 BPC. (E) Structures depicting the helix-loop-helix motif of CRL4 SRs (DCAF12 and AMBRA1) bound to DDB1 through contacts made in the BPA and BPC cleft of DDB1. CRBN is distinct from other CRL4 SRs in that it does not utilize a helix-loop-helix motif but instead a 7-helical bundle to bind to both BPA and BPC. (F) Sequences of helix-loop-helix motif DDB1-binding proteins. The 2 distinct helices of the helix-loop-helix motif are shaded in 2 shades of yellow (left H-box, right second helix). Regions were highlighted based on experimentally solved structures and AlphaFold structures.

Article Snippet: The Tabula Sapiens dataset (version 1 and version 2) was used for single-cell RNA-seq analyses., Experimental and predicted protein structures were obtained from RSCB Protein Data Bank (RSCB PDB), AlphaFold Protein Structure Database (Google DeepMind and EMBL-EBI, https://alphafold.ebi.ac.uk ) and AlphaFold Server (Google DeepMind, https://alphafoldserver.com/ ).,

Techniques: Sequencing, High Throughput Screening Assay, Binding Assay