6FGA: TRIM21 E3 ligase, RING domain
Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1. Determined by X-ray diffraction at 2.82 Å resolution. Released 12 Jun 2019.
- Method
- X-ray diffraction
- Resolution
- 2.82 Å
- Organism
- Homo sapiens
- Chains
- 15
- Atoms
- 13,206
- Mol. weight
- 214.16 kDa
- Ligands
- ZN
- Released
- 12 Jun 2019
Explore 6FGA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6FGA contains 74 α-helices and 114 β-strands across 15 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: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 1 |
| β-strand | 22 | 1 | 1 |
| β-strand | 26-28 | 3 | 2 |
| β-strand | 34-36 | 3 | 2 |
| α-helix | 37-43 | 7 | |
| β-strand | 50 | 1 | 3 |
| β-strand | 57 | 1 | 3 |
| β-strand | 64-65 | 2 | 2 |
| α-helix | 67-80 | 14 | |
Chain B: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 4 |
| β-strand | 22 | 1 | 4 |
| β-strand | 26-28 | 3 | 5 |
| β-strand | 34-36 | 3 | 5 |
| α-helix | 37-45 | 9 | |
| β-strand | 50 | 1 | 6 |
| β-strand | 57 | 1 | 6 |
| β-strand | 64-65 | 2 | 5 |
| α-helix | 67-80 | 14 | |
Chain C: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| β-strand | 15 | 1 | 7 |
| β-strand | 22 | 1 | 7 |
| β-strand | 26-28 | 3 | 8 |
| β-strand | 34-36 | 3 | 8 |
| α-helix | 37-45 | 9 | |
| β-strand | 50 | 1 | 9 |
| β-strand | 57 | 1 | 9 |
| β-strand | 64-65 | 2 | 8 |
| α-helix | 67-81 | 15 | |
Chain D: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| β-strand | 15 | 1 | 10 |
| β-strand | 22 | 1 | 10 |
| β-strand | 26-28 | 3 | 11 |
| β-strand | 34-36 | 3 | 11 |
| α-helix | 37-44 | 8 | |
| β-strand | 50 | 1 | 12 |
| β-strand | 57 | 1 | 12 |
| β-strand | 64-65 | 2 | 11 |
| α-helix | 67-78 | 12 | |
Chain E: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 13 |
| β-strand | 22 | 1 | 13 |
| β-strand | 26-28 | 3 | 14 |
| β-strand | 34-36 | 3 | 14 |
| α-helix | 37-45 | 9 | |
| β-strand | 50 | 1 | 15 |
| β-strand | 56 | 1 | 16 |
| β-strand | 57 | 1 | 15 |
| β-strand | 64-65 | 2 | 14 |
| α-helix | 67-81 | 15 | |
Chain F: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 17 |
| β-strand | 22 | 1 | 17 |
| β-strand | 26-28 | 3 | 18 |
| β-strand | 34-36 | 3 | 18 |
| α-helix | 37-45 | 9 | |
| β-strand | 50 | 1 | 19 |
| β-strand | 56 | 1 | 16 |
| β-strand | 57 | 1 | 19 |
| α-helix | 60-62 | 3 | |
| β-strand | 64-65 | 2 | 18 |
| α-helix | 67-81 | 15 | |
Chain G: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 20 |
| β-strand | 22 | 1 | 20 |
| β-strand | 26-28 | 3 | 21 |
| β-strand | 34-36 | 3 | 21 |
| α-helix | 37-43 | 7 | |
| β-strand | 50 | 1 | 22 |
| β-strand | 57 | 1 | 22 |
| β-strand | 64-65 | 2 | 21 |
| α-helix | 67-81 | 15 | |
Chain H: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15 | 1 | 23 |
| β-strand | 22 | 1 | 23 |
| β-strand | 26-28 | 3 | 24 |
| β-strand | 34-36 | 3 | 24 |
| α-helix | 37-44 | 8 | |
| β-strand | 50 | 1 | 25 |
| β-strand | 57 | 1 | 25 |
| β-strand | 64-65 | 2 | 24 |
| α-helix | 67-81 | 15 | |
5 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 TRIM21 | A, B, C, D, E, F, G, H | protein | 101 | Homo sapiens | P19474 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 E1 | I, J, K, L, M, N, O | protein | 158 | Homo sapiens | P51965 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA
>6FGA_1 E3 ubiquitin-protein ligase TRIM21 (chains A, B, C, D, E, F, G, H)
GSHMASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQR
FLLKNLRPNRQLANMVNNLKEISQEAREGTQGERCAVHGER
Sequence of entity 2 (I, J, K, L, M, N, O), FASTA
>6FGA_2 Ubiquitin-conjugating enzyme E2 E1 (chains I, J, K, L, M, N, O)
GSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGV
FFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSL
LTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 16 |
Water and common crystallization additives (GOL) are not listed.
Primary citation
E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2. Anandapadamanaban, M., Kyriakidis, N.C., Csizmok, V. et al. J Biol Chem (2019) 294:11404-11419. DOI 10.1074/jbc.RA119.008485 · PubMed
Other PDB entries of the same protein (UniProt P19474 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 32QO 1.3 Å, Human TRIM21 PRYSPRY domain in complex with compound 28 (Z38)
- 9PLM 1.32 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-021)
- 32QL 1.4 Å, Human TRIM21 PRYSPRY domain in complex with HGC652
- 9QBA 1.45 Å, Human TRIM21 PRYSPRY domain in complex with AL236
- 9II5 1.49 Å, Crystal structure of human TRIM21 PRYSPRY in complex with compound 1
- 32QM 1.5 Å, Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
- 8Y58 1.6 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine.
- 9PLL 1.6 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-056)
- 8Y5B 1.74 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine.
- 32QN 1.8 Å, Human TRIM21 PRYSPRY domain in complex with compound 29 (Z37)
- 8Y59 1.89 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine.
- 5OLM 1.95 Å, TRIM21
Browse structure collections
About this viewer
MolViewer shows 6FGA directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.