3IXS: E3 ubiquitin-protein ligase RING2
Ring1B C-terminal domain/RYBP C-terminal domain Complex. Determined by X-ray diffraction at 1.7 Å resolution. Released 25 Aug 2010.
- Method
- X-ray diffraction
- Resolution
- 1.7 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 6,935
- Mol. weight
- 100.79 kDa
- Ligands
- NHE
- Released
- 25 Aug 2010
Explore 3IXS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3IXS contains 33 α-helices and 62 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 226-232 | 7 | 1 |
| β-strand | 246-250 | 5 | 1 |
| β-strand | 255 | 1 | 2 |
| α-helix | 256-271 | 16 | |
| α-helix | 283-285 | 3 | |
| α-helix | 288-290 | 3 | |
| β-strand | 291-296 | 6 | 1 |
| β-strand | 302-304 | 3 | 1 |
| α-helix | 305-306 | 2 | |
| β-strand | 310 | 1 | 2 |
| α-helix | 311-314 | 4 | |
| α-helix | 315-319 | 5 | |
| β-strand | 321 | 1 | 3 |
| β-strand | 325-331 | 7 | 1 |
Chains B, D and J: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 151-163 | 13 | 1 |
| β-strand | 166-175 | 10 | 1 |
Chain C: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-232 | 8 | 1 |
| β-strand | 246-251 | 6 | 1 |
| β-strand | 255 | 1 | 4 |
| α-helix | 256-275 | 20 | |
| α-helix | 280-282 | 3 | |
| α-helix | 288-290 | 3 | |
| β-strand | 291-296 | 6 | 1 |
| β-strand | 302-304 | 3 | 1 |
| α-helix | 305-306 | 2 | |
| β-strand | 309 | 1 | 5 |
| β-strand | 310 | 1 | 4 |
| α-helix | 311-318 | 8 | |
| α-helix | 324 | 1 | |
| β-strand | 325-331 | 7 | 1 |
Chain E: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 226-232 | 7 | 6 |
| β-strand | 246-250 | 5 | 6 |
| β-strand | 255 | 1 | 7 |
| α-helix | 256-271 | 16 | |
| α-helix | 288-290 | 3 | |
| β-strand | 291-296 | 6 | 6 |
| β-strand | 302-304 | 3 | 6 |
| α-helix | 305-306 | 2 | |
| β-strand | 310 | 1 | 7 |
| α-helix | 311-314 | 4 | |
| α-helix | 315-319 | 5 | |
| β-strand | 321 | 1 | 5 |
| β-strand | 325-331 | 7 | 6 |
Chains F and L: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 151 | 1 | 8 |
| α-helix | 153-155 | 3 | |
| β-strand | 157-163 | 7 | 6 |
| β-strand | 166-173 | 8 | 6 |
| β-strand | 175 | 1 | 8 |
Chain G: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-232 | 8 | 6 |
| β-strand | 246-251 | 6 | 6 |
| β-strand | 255 | 1 | 9 |
| α-helix | 256-272 | 17 | |
| α-helix | 288-290 | 3 | |
| β-strand | 291-296 | 6 | 6 |
| β-strand | 302-304 | 3 | 6 |
| α-helix | 305-306 | 2 | |
| β-strand | 309 | 1 | 3 |
| β-strand | 310 | 1 | 9 |
| α-helix | 311-318 | 8 | |
| β-strand | 325-331 | 7 | 6 |
Chain H: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 145-148 | 4 | |
| β-strand | 151-163 | 13 | 6 |
| β-strand | 166-175 | 10 | 6 |
| α-helix | 176-178 | 3 | |
Chain I: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-232 | 8 | 10 |
| β-strand | 246-251 | 6 | 10 |
| β-strand | 255 | 1 | 11 |
| α-helix | 256-272 | 17 | |
| β-strand | 291-296 | 6 | 10 |
| β-strand | 302-304 | 3 | 10 |
| α-helix | 305-306 | 2 | |
| β-strand | 310 | 1 | 11 |
| α-helix | 311-314 | 4 | |
| α-helix | 315-319 | 5 | |
| β-strand | 325-331 | 7 | 10 |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| E3 ubiquitin-protein ligase RING2 | A, C, E, G, I, K | protein | 111 | Homo sapiens | Q99496 (AlphaFold model) |
| RING1 and YY1-binding protein | B, D, F, H, J, L | protein | 37 | Homo sapiens | Q8N488 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K), FASTA
>3IXS_1 E3 ubiquitin-protein ligase RING2 (chains A, C, E, G, I, K)
ASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMN
LDTASEKQYTIYIATASGQFTVLDGSFSLELVSEKYWKVNKPMELYYAPTK
Sequence of entity 2 (B, D, F, H, J, L), FASTA
>3IXS_2 RING1 and YY1-binding protein (chains B, D, F, H, J, L)
GTRPRLKNVDRSTAQQLAVTVGNVTVIITDFKEKTRS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NHE | 2-[N-cyclohexylamino]ethane sulfonic acid | C8 H17 N O3 S | 1 |
Water and common crystallization additives (EDO) are not listed.
Primary citation
Polycomb Group Targeting through Different Binding Partners of RING1B C-Terminal Domain. Wang, R., Taylor, A.B., Leal, B.Z. et al. Structure (2010) 18:966-975. DOI 10.1016/j.str.2010.04.013 · PubMed
Other PDB entries of the same protein (UniProt Q99496 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3GS2 1.7 Å, Ring1B C-terminal domain/Cbx7 Cbox Complex
- 6WI7 1.7 Å, RING1B-BMI1 fusion in closed conformation
- 3H8H 2.0 Å, Structure of the C-terminal domain of human RNF2/RING1B;
- 4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
- 2H0D 2.5 Å, Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex
- 3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure
- 28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
- 9DBY 2.8 Å, ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
- 9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
- 8PP7 2.91 Å, human RYBP-PRC1 bound to mononucleosome
- 9DGG 2.98 Å, ncPRC1RYBP bound to unmodified nucleosome
- 9V6S 3.0 Å, Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp…
Browse structure collections
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