2ZVN: UBC protein
NEMO CoZi domain incomplex with diubiquitin in P212121 space group. Determined by X-ray diffraction at 3.0 Å resolution. Released 24 Mar 2009.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 8
- Atoms
- 7,598
- Mol. weight
- 110.4 kDa
- Released
- 24 Mar 2009
Explore 2ZVN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2ZVN contains 31 α-helices and 57 β-strands across 8 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: 4 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 1 |
| β-strand | 12-15 | 4 | 1 |
| β-strand | 22 | 1 | 2 |
| α-helix | 23-33 | 11 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 1 |
| β-strand | 48-49 | 2 | 1 |
| β-strand | 55 | 1 | 2 |
| β-strand | 66-71 | 6 | 1 |
| β-strand | 78-82 | 5 | 3 |
| β-strand | 88-92 | 5 | 3 |
| β-strand | 98 | 1 | 4 |
| α-helix | 99-110 | 12 | |
| β-strand | 118-121 | 4 | 3 |
| β-strand | 124-125 | 2 | 3 |
| α-helix | 126 | 1 | |
| β-strand | 131 | 1 | 4 |
| β-strand | 142-146 | 5 | 3 |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 253-288 | 36 | |
| α-helix | 291-333 | 43 | |
Chain C: 6 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 9 |
| β-strand | 12-16 | 5 | 9 |
| β-strand | 22 | 1 | 10 |
| α-helix | 24-33 | 10 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 9 |
| β-strand | 48-49 | 2 | 9 |
| β-strand | 55 | 1 | 10 |
| β-strand | 66-71 | 6 | 9 |
| β-strand | 77-82 | 6 | 11 |
| β-strand | 88-93 | 6 | 11 |
| β-strand | 98 | 1 | 12 |
| α-helix | 99-110 | 12 | |
| α-helix | 114-116 | 3 | |
| β-strand | 119-121 | 3 | 11 |
| β-strand | 124-125 | 2 | 11 |
| β-strand | 131 | 1 | 12 |
| α-helix | 133-135 | 3 | |
| α-helix | 137-138 | 2 | |
| β-strand | 142-145 | 4 | 11 |
Chain D: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 255-288 | 34 | |
| α-helix | 290-334 | 45 | |
Chain E: 6 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 13 |
| β-strand | 12-16 | 5 | 13 |
| β-strand | 22 | 1 | 14 |
| α-helix | 23-32 | 10 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-44 | 4 | 13 |
| β-strand | 49 | 1 | 13 |
| β-strand | 55 | 1 | 14 |
| α-helix | 57-59 | 3 | |
| β-strand | 65 | 1 | 13 |
| β-strand | 68-71 | 4 | 13 |
| β-strand | 78-82 | 5 | 15 |
| β-strand | 88-92 | 5 | 15 |
| β-strand | 98 | 1 | 16 |
| α-helix | 99-110 | 12 | |
| α-helix | 114-116 | 3 | |
| β-strand | 119-120 | 2 | 15 |
| β-strand | 125 | 1 | 15 |
| α-helix | 126-127 | 2 | |
| β-strand | 131 | 1 | 16 |
| β-strand | 142-145 | 4 | 15 |
Chain F: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 253-288 | 36 | |
| α-helix | 291-336 | 46 | |
Chain G: 7 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 5 |
| β-strand | 12-16 | 5 | 5 |
| β-strand | 22 | 1 | 6 |
| α-helix | 23-32 | 10 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 5 |
| β-strand | 48-49 | 2 | 5 |
| β-strand | 55 | 1 | 6 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 5 |
| β-strand | 78-82 | 5 | 7 |
| β-strand | 88-92 | 5 | 7 |
| β-strand | 98 | 1 | 8 |
| α-helix | 99-110 | 12 | |
| α-helix | 114-116 | 3 | |
| β-strand | 119-120 | 2 | 7 |
| β-strand | 125 | 1 | 7 |
| α-helix | 126-127 | 2 | |
| β-strand | 131 | 1 | 8 |
| α-helix | 132-135 | 4 | |
| β-strand | 142-145 | 4 | 7 |
Chain H: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 255-287 | 33 | |
| α-helix | 290-335 | 46 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| UBC protein | A, C, E, G | protein | 154 | Homo sapiens | P0CG48 (AlphaFold model) |
| NF-kappa-B essential modulator | B, D, F, H | protein | 87 | Mus musculus | O88522 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>2ZVN_1 UBC protein (chains A, C, E, G)
GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQR
LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Sequence of entity 2 (B, D, F, H), FASTA
>2ZVN_2 NF-kappa-B essential modulator (chains B, D, F, H)
GSLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERH
AREKLVEKKEYLQEQLEQLQREFNKLK
Primary citation
Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Rahighi, S., Ikeda, F., Kawasaki, M. et al. Cell (2009) 136:1098-1109. DOI 10.1016/j.cell.2009.03.007 · PubMed
Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
- 1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
- 5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
- 2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
- 4HK2 1.4 Å, U7Ub25.2540
- 9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
- 1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
- 4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
- 7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
- 5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
- 9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
- 9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant
Browse structure collections
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