Npl4 in complex with Ufd1. Determined by X-ray diffraction at 1.58 Å resolution. Released 25 Dec 2019.
Explore 6JWJ in 3D Show helices and sheets RCSB PDB PDBe
6JWJ contains 25 α-helices and 28 β-strands across 2 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 114-116 | 3 | |
| α-helix | 117-123 | 7 | |
| β-strand | 129 | 1 | 1 |
| α-helix | 150 | 1 | |
| β-strand | 151 | 1 | 1 |
| α-helix | 152 | 1 | |
| α-helix | 156-161 | 6 | |
| β-strand | 167-168 | 2 | 2 |
| α-helix | 169-180 | 12 | |
| α-helix | 184 | 1 | |
| α-helix | 188-189 | 2 | |
| β-strand | 193 | 1 | 3 |
| β-strand | 224-226 | 3 | 4 |
| β-strand | 231-232 | 2 | 2 |
| β-strand | 236-239 | 4 | 5 |
| α-helix | 242-255 | 14 | |
| β-strand | 260-270 | 11 | 5 |
| β-strand | 276-285 | 10 | 5 |
| α-helix | 286-287 | 2 | |
| β-strand | 290-292 | 3 | 6 |
| β-strand | 295-297 | 3 | 6 |
| α-helix | 300-316 | 17 | |
| β-strand | 320-328 | 9 | 5 |
| β-strand | 331 | 1 | 7 |
| β-strand | 339 | 1 | 7 |
| α-helix | 352-364 | 13 | |
| β-strand | 366-368 | 3 | 8 |
| β-strand | 372 | 1 | 3 |
| β-strand | 376-379 | 4 | 8 |
| β-strand | 382-388 | 7 | 5 |
| β-strand | 394-401 | 8 | 5 |
| α-helix | 403-410 | 8 | |
| β-strand | 414-415 | 2 | 9 |
| β-strand | 417 | 1 | 10 |
| β-strand | 422-425 | 4 | 9 |
| α-helix | 426-428 | 3 | |
| β-strand | 437-442 | 6 | 4 |
| β-strand | 448-452 | 5 | 4 |
| β-strand | 456-458 | 3 | 9 |
| α-helix | 459-462 | 4 | |
| β-strand | 463-469 | 7 | 5 |
| α-helix | 488-489 | 2 | |
| α-helix | 493-495 | 3 | |
| α-helix | 501-512 | 12 | |
| α-helix | 517-524 | 8 | |
| α-helix | 527-535 | 9 | |
| α-helix | 541-552 | 12 | |
| α-helix | 557-565 | 9 | |
| α-helix | 567-577 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 289-290 | 2 | |
| β-strand | 291 | 1 | 10 |
| α-helix | 294-295 | 2 | |
| β-strand | 298-300 | 3 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Nuclear protein localization protein 4 | A | protein | 473 | Saccharomyces cerevisiae S288C | P33755 (AlphaFold model) |
| Peptide from Ubiquitin fusion degradation protein 1 | C | protein | 23 | Saccharomyces cerevisiae S288C | P53044 (AlphaFold model) |
>6JWJ_1 Nuclear protein localization protein 4 (chains A) GPLGSIKELAVDEELAAADGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHI SFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQ QQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEP PQHDEQDGLTMDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDS FFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEA LVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLT HGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNF HLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG
>6JWJ_2 Peptide from Ubiquitin fusion degradation protein 1 (chains C) GPGHMEPAKLDLPEGQLFFGFPM
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 2 |
Water and common crystallization additives (GOL) are not listed.
Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Sato, Y., Tsuchiya, H., Yamagata, A. et al. Nat Commun (2019) 10:5708-5708. DOI 10.1038/s41467-019-13697-y · PubMed
Other PDB entries of the same protein (UniProt P33755 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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