Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide containing the DxE cargo sorting signal of yeast Sys1 protein. Determined by X-ray diffraction at 2.6 Å resolution. Released 19 Aug 2003.
Explore 1PD1 in 3D Show helices and sheets RCSB PDB PDBe
1PD1 contains 40 α-helices and 41 β-strands across 1 chain. 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 |
|---|---|---|---|
| β-strand | 140-142 | 3 | 1 |
| α-helix | 143-145 | 3 | |
| α-helix | 151-155 | 5 | |
| α-helix | 157-160 | 4 | |
| α-helix | 165-167 | 3 | |
| β-strand | 182-184 | 3 | 2 |
| β-strand | 186 | 1 | 3 |
| β-strand | 189-190 | 2 | 4 |
| α-helix | 193-199 | 7 | |
| β-strand | 204-207 | 4 | 2 |
| α-helix | 219-221 | 3 | |
| β-strand | 222-223 | 2 | 5 |
| β-strand | 230 | 1 | 6 |
| α-helix | 236 | 1 | |
| β-strand | 237 | 1 | 6 |
| α-helix | 238 | 1 | |
| β-strand | 243-245 | 3 | 7 |
| β-strand | 250-252 | 3 | 7 |
| β-strand | 259-261 | 3 | 7 |
| α-helix | 262-263 | 2 | |
| α-helix | 264-267 | 4 | |
| α-helix | 277-279 | 3 | |
| α-helix | 281-284 | 4 | |
| β-strand | 287-291 | 5 | 5 |
| α-helix | 294-296 | 3 | |
| α-helix | 302-304 | 3 | |
| β-strand | 305-311 | 7 | 8 |
| α-helix | 314-319 | 6 | |
| α-helix | 321-332 | 12 | |
| β-strand | 344-350 | 7 | 8 |
| β-strand | 354-358 | 5 | 8 |
| α-helix | 362-364 | 3 | |
| β-strand | 374-378 | 5 | 8 |
| β-strand | 390 | 1 | 8 |
| β-strand | 393-395 | 3 | 8 |
| α-helix | 400-413 | 14 | |
| α-helix | 424-435 | 12 | |
| β-strand | 440-446 | 7 | 8 |
| α-helix | 482-493 | 12 | |
| β-strand | 495-503 | 9 | 8 |
| α-helix | 509-517 | 9 | |
| β-strand | 523-527 | 5 | 8 |
| α-helix | 534-549 | 16 | |
| β-strand | 553-562 | 10 | 5 |
| β-strand | 566-572 | 7 | 2 |
| β-strand | 576 | 1 | 5 |
| β-strand | 583-588 | 6 | 5 |
| β-strand | 594-600 | 7 | 2 |
| α-helix | 603-604 | 2 | |
| β-strand | 608-619 | 12 | 5 |
| β-strand | 623-634 | 12 | 5 |
| β-strand | 635-636 | 2 | 4 |
| α-helix | 639-644 | 6 | |
| β-strand | 646 | 1 | 3 |
| α-helix | 648-663 | 16 | |
| α-helix | 668-689 | 22 | |
| β-strand | 702-704 | 3 | 1 |
| α-helix | 705-707 | 3 | |
| α-helix | 710-719 | 10 | |
| α-helix | 730-742 | 13 | |
| α-helix | 745-752 | 8 | |
| β-strand | 755-758 | 4 | 9 |
| β-strand | 769 | 1 | 10 |
| α-helix | 780 | 1 | |
| β-strand | 781 | 1 | 10 |
| α-helix | 782-786 | 5 | |
| β-strand | 787 | 1 | 9 |
| α-helix | 791-793 | 3 | |
| β-strand | 799-803 | 5 | 9 |
| β-strand | 807-812 | 6 | 9 |
| α-helix | 818-825 | 8 | |
| α-helix | 830-832 | 3 | |
| β-strand | 836-837 | 2 | 9 |
| α-helix | 839-841 | 3 | |
| α-helix | 847-858 | 12 | |
| α-helix | 869 | 1 | |
| β-strand | 870-875 | 6 | 9 |
| α-helix | 889-901 | 13 | |
| β-strand | 907 | 1 | 11 |
| β-strand | 910 | 1 | 11 |
| α-helix | 913-923 | 11 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Protein transport protein Sec24 | A | protein | 810 | Saccharomyces cerevisiae | P40482 (AlphaFold model) |
| DxE cargo sorting signal peptide of yeast Sys1 protein | B | protein | 9 |
>1PD1_1 Protein transport protein Sec24 (chains A) AAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSN ASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRS YMNPFVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEY TLRQPPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHY FKIPLDSENNEESADQINMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQS NLITNFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLL SCQDSFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPND IVKFSTEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLF EVNVDESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYN SKAVEKALNSSLDDARVLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHS LTKHMAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGE ATGTIVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIG KQEIPVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRL WASSTLVEDKILNNESYREFLQIMKARISK
>1PD1_2 DxE cargo sorting signal peptide of yeast Sys1 protein (chains B) QLKDLESQI
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 1 |
SNARE selectivity of the COPII coat. Mossessova, E., Bickford, L.C., Goldberg, J. Cell (2003) 114:483-495. DOI 10.1016/S0092-8674(03)00608-1 · PubMed
Other PDB entries of the same protein (UniProt P40482 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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