2DZN: Crystal structure analysis of yeast Nas6p
Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 Jul 2007.
- Method
- X-ray diffraction
- Resolution
- 2.2 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 7,346
- Mol. weight
- 104.57 kDa
- Released
- 17 Jul 2007
Explore 2DZN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2DZN contains 61 α-helices and 12 β-strands across 6 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: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-11 | 7 | |
| α-helix | 15-24 | 10 | |
| α-helix | 26-28 | 3 | |
| α-helix | 39-45 | 7 | |
| α-helix | 49-57 | 9 | |
| α-helix | 64-66 | 3 | |
| α-helix | 75-82 | 8 | |
| α-helix | 85-92 | 8 | |
| α-helix | 110-116 | 7 | |
| α-helix | 120-128 | 9 | |
| α-helix | 143-149 | 7 | |
| α-helix | 153-157 | 5 | |
| α-helix | 158-162 | 5 | |
| α-helix | 177-183 | 7 | |
| α-helix | 187-197 | 11 | |
| β-strand | 204 | 1 | 1 |
| β-strand | 210 | 1 | 1 |
| α-helix | 211-214 | 4 | |
| α-helix | 220-225 | 6 | |
Chain B: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 361-362 | 2 | 2 |
| α-helix | 380-396 | 17 | |
| β-strand | 401-402 | 2 | 2 |
| α-helix | 404-412 | 9 | |
Chain C: 19 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-11 | 7 | |
| α-helix | 15-24 | 10 | |
| α-helix | 26-30 | 5 | |
| α-helix | 39-45 | 7 | |
| α-helix | 49-57 | 9 | |
| α-helix | 64-66 | 3 | |
| α-helix | 75-82 | 8 | |
| α-helix | 85-92 | 8 | |
| α-helix | 97-98 | 2 | |
| α-helix | 110-116 | 7 | |
| α-helix | 120-128 | 9 | |
| α-helix | 143-150 | 8 | |
| α-helix | 153-163 | 11 | |
| α-helix | 164-166 | 3 | |
| α-helix | 177-183 | 7 | |
| α-helix | 187-191 | 5 | |
| α-helix | 192-196 | 5 | |
| β-strand | 204 | 1 | 3 |
| β-strand | 210 | 1 | 3 |
| α-helix | 211-214 | 4 | |
| α-helix | 218-225 | 8 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 351-359 | 9 | |
| β-strand | 362 | 1 | 4 |
| α-helix | 368-372 | 5 | |
| α-helix | 380-396 | 17 | |
| β-strand | 402 | 1 | 4 |
| α-helix | 404-413 | 10 | |
Chain E: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-11 | 7 | |
| α-helix | 15-24 | 10 | |
| α-helix | 39-45 | 7 | |
| α-helix | 49-58 | 10 | |
| α-helix | 64-66 | 3 | |
| α-helix | 75-82 | 8 | |
| α-helix | 85-92 | 8 | |
| α-helix | 110-116 | 7 | |
| α-helix | 120-128 | 9 | |
| α-helix | 143-149 | 7 | |
| α-helix | 153-160 | 8 | |
| α-helix | 177-183 | 7 | |
| α-helix | 187-197 | 11 | |
| β-strand | 204 | 1 | 5 |
| β-strand | 210 | 1 | 5 |
| α-helix | 211-214 | 4 | |
| α-helix | 218-227 | 10 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 350-357 | 8 | |
| β-strand | 362 | 1 | 6 |
| α-helix | 369-374 | 6 | |
| α-helix | 380-395 | 16 | |
| β-strand | 402 | 1 | 6 |
| α-helix | 404-415 | 12 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Probable 26S proteasome regulatory subunit p28 | A, C, E | protein | 228 | Saccharomyces cerevisiae | P50086 (AlphaFold model) |
| 26S protease regulatory subunit 6B homolog | B, D, F | protein | 82 | Saccharomyces cerevisiae | P33298 (AlphaFold model) |
Sequence of entity 1 (A, C, E), FASTA
>2DZN_1 Probable 26S proteasome regulatory subunit p28 (chains A, C, E)
MSNYPLHQACMENEFFKVQELLHSKPSLLLQKDQDGRIPLHWSVSFQAHEITSFLLSKME
NVNLDDYPDDSGWTPFHIACSVGNLEVVKSLYDRPLKPDLNKITNQGVTCLHLAVGKKWF
EVSQFLIENGASVRIKDKFNQIPLHRAASVGSLKLIELLCGLGKSAVNWQDKQGWTPLFH
ALAEGHGDAAVLLVEKYGAEYDLVDNKGAKAEDVALNEQVKKFFLNNV
Sequence of entity 2 (B, D, F), FASTA
>2DZN_2 26S protease regulatory subunit 6B homolog (chains B, D, F)
MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSD
LEEAYATQVKTDNTVDKFDFYK
Primary citation
Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Nakamura, Y., Umehara, T., Tanaka, A. et al. Biochem Biophys Res Commun (2007) 359:503-509. DOI 10.1016/j.bbrc.2007.05.138 · PubMed
Other PDB entries of the same protein (UniProt P50086 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1IXV 2.3 Å, Crystal Structure Analysis of homolog of oncoprotein gankyrin, an interactor of Rb and…
- 1WG0 2.53 Å, Structural comparison of Nas6p protein structures in two different crystal forms
- 2DZO 3.0 Å, Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3
- 35ZW 3.31 Å, yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2-Rpt3-Rpt4-Rpt5…
- 36BM 3.82 Å, yeast 26S proteasome base assembly intermediate, base-Hsm3-Nas6 with Rpt4-EQ
- 36BL 3.91 Å, yeast 26S proteasome base assembly intermediate, base-Rpn14-Hsm3-Nas6(2) with Rpt4-EQ
- 36BD 3.93 Å, yeast 26S proteasome base assembly intermediate, base-Rpn14-Hsm3-Nas6 with Rpt4-EQ
- 36AX 4.87 Å, yeast 26S proteasome base assembly intermediate, base-Nas2-Rpn14-Hsm3-Nas6 with Rpt4-EQ
Browse structure collections
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