7P47: E3 ligase Smc5/Nse2
Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic. Determined by X-ray diffraction at 3.31 Å resolution. Released 24 Nov 2021.
- Method
- X-ray diffraction
- Resolution
- 3.31 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 5
- Atoms
- 4,561
- Mol. weight
- 80.71 kDa
- Ligands
- ZN
- Released
- 24 Nov 2021
Explore 7P47 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7P47 contains 22 α-helices and 27 β-strands across 5 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: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-49 | 26 | |
| α-helix | 58-79 | 22 | |
| α-helix | 142-155 | 14 | |
| α-helix | 159-161 | 3 | |
| β-strand | 178-179 | 2 | 3 |
| β-strand | 183 | 1 | 4 |
| β-strand | 190 | 1 | 4 |
| α-helix | 191 | 1 | |
| β-strand | 194-197 | 4 | 5 |
| β-strand | 203-205 | 3 | 5 |
| α-helix | 206-212 | 7 | |
| β-strand | 218-220 | 3 | 6 |
| β-strand | 229-231 | 3 | 6 |
| α-helix | 232-234 | 3 | |
| β-strand | 235-237 | 3 | 5 |
| α-helix | 239-253 | 15 | |
| β-strand | 264-265 | 2 | 7 |
Chain B: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 330-360 | 31 | |
| α-helix | 742-768 | 27 | |
| α-helix | 769-771 | 3 | |
Chain C: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-16 | 13 | |
| β-strand | 25-30 | 6 | 1 |
| β-strand | 36-46 | 11 | 1 |
| α-helix | 47-48 | 2 | |
| β-strand | 57-63 | 7 | 1 |
| α-helix | 72-73 | 2 | |
| β-strand | 74-76 | 3 | 1 |
| β-strand | 86 | 1 | 1 |
| β-strand | 91-92 | 2 | 1 |
| β-strand | 94 | 1 | 2 |
| α-helix | 95-97 | 3 | |
| α-helix | 109-120 | 12 | |
| α-helix | 132-139 | 8 | |
| α-helix | 141-154 | 14 | |
Chain D: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-29 | 7 | 3 |
| β-strand | 34-40 | 7 | 3 |
| α-helix | 46-56 | 11 | |
| β-strand | 64-67 | 4 | 3 |
| β-strand | 70-71 | 2 | 3 |
| β-strand | 87-92 | 6 | 3 |
| α-helix | 93-94 | 2 | |
| β-strand | 97 | 1 | 2 |
Chain E: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-29 | 7 | 7 |
| β-strand | 36-40 | 5 | 7 |
| α-helix | 46-56 | 11 | |
| α-helix | 60-62 | 3 | |
| β-strand | 64-67 | 4 | 7 |
| β-strand | 70-71 | 2 | 7 |
| β-strand | 87-92 | 6 | 7 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Structural maintenance of chromosomes protein 5 | B | protein | 84 | Saccharomyces cerevisiae | Q08204 (AlphaFold model) |
| SUMO-conjugating enzyme UBC9 | C | protein | 165 | Saccharomyces cerevisiae | P50623 (AlphaFold model) |
| E3 SUMO-protein ligase MMS21 | A | protein | 214 | Saccharomyces cerevisiae | P38632 (AlphaFold model) |
| Ubiquitin-like protein SMT3 | D, E | protein | 121 | Saccharomyces cerevisiae | Q12306 (AlphaFold model) |
Sequence of entity 1 (B), FASTA
>7P47_1 Structural maintenance of chromosomes protein 5 (chains B)
MGTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYRGRTGTRKDVSQKIKDIDDQIQQ
LLLKQRHLLSKMASSMKSLKNCQK
Sequence of entity 2 (C), FASTA
>7P47_2 SUMO-conjugating enzyme UBC9 (chains C)
MSSLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPI
TVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLL
DSPNPNSPKQEPAWRSFSRNKAEYDKKVLLQARQYSKGYHHHHHH
Sequence of entity 3 (A), FASTA
>7P47_3 E3 SUMO-protein ligase MMS21 (chains A)
MGSSHHHHHHSSGLVPRGSHMLEARDLSNIYQQCYKQIDETINQLVDSTSPSTIGIEEQV
ADITSTYKLLSTYESESNSGTATMVNNTDTLKILKVLPYIWNDPTCVIPDLQNPADEDDL
QIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR
DFVRDPIMELRCKIAKMKESQEQDKRSSQAIDVL
Sequence of entity 4 (D, E), FASTA
>7P47_4 Ubiquitin-like protein SMT3 (chains D, E)
MGSSHHHHHHSSGLVPRGSHMASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFF
KIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG
G
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural basis for the E3 ligase activity enhancement of yeast Nse2 by SUMO-interacting motifs. Varejao, N., Lascorz, J., Codina-Fabra, J. et al. Nat Commun (2021) 12:7013-7013. DOI 10.1038/s41467-021-27301-9 · PubMed
Other PDB entries of the same protein (UniProt Q08204 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3HTK 2.31 Å, Crystal structure of Mms21 and Smc5 complex
- 8HQS 3.2 Å, Cryo-EM structure of 8-subunit Smc5/6 head region
- 7TVE 3.8 Å, ATP and DNA bound SMC5/6 core complex
- 8T8F 4.8 Å, Smc5/6 8mer
- 8WJN 5.58 Å, Cryo-EM structure of 6-subunit Smc5/6 head region
- 7YQH 5.6 Å, Cryo-EM structure of 8-subunit Smc5/6
- 8I4V 5.97 Å, Cryo-EM structure of 5-subunit Smc5/6 arm region
- 8I4W 6.01 Å, Cryo-EM structure of 5-subunit Smc5/6 head region
- 8I21 6.02 Å, Cryo-EM structure of 6-subunit Smc5/6 arm region
- 8WJO 6.04 Å, Cryo-EM structure of 8-subunit Smc5/6 arm region
- 8WJL 6.15 Å, Cryo-EM structure of 6-subunit Smc5/6 hinge region
- 7YLM 6.17 Å, Cryo-EM structure of 8-subunit Smc5/6 hinge region
Browse structure collections
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