Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum. Determined by electron microscopy at 2.84 Å resolution. Released 20 Dec 2023.
Explore 8K9Q in 3D Show helices and sheets RCSB PDB PDBe
8K9Q contains 48 α-helices and 35 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 |
|---|---|---|---|
| α-helix | 147-168 | 22 | |
| β-strand | 186-188 | 3 | 1 |
| β-strand | 204-208 | 5 | 1 |
| β-strand | 211 | 1 | 2 |
| β-strand | 214 | 1 | 2 |
| β-strand | 219 | 1 | 3 |
| β-strand | 222-227 | 6 | 1 |
| α-helix | 234-237 | 4 | |
| α-helix | 238-250 | 13 | |
| α-helix | 252-254 | 3 | |
| α-helix | 256-261 | 6 | |
| β-strand | 266-272 | 7 | 1 |
| α-helix | 278-280 | 3 | |
| α-helix | 282-300 | 19 | |
| β-strand | 309 | 1 | 3 |
| α-helix | 316-318 | 3 | |
| β-strand | 321-326 | 6 | 1 |
| α-helix | 329-336 | 8 | |
| β-strand | 347-353 | 7 | 1 |
| α-helix | 366-384 | 19 | |
| β-strand | 397-402 | 6 | 1 |
| α-helix | 404-406 | 3 | |
| α-helix | 412-415 | 4 | |
| β-strand | 428-430 | 3 | 1 |
| α-helix | 445-448 | 4 | |
| α-helix | 450-460 | 11 | |
| α-helix | 475-486 | 12 | |
| α-helix | 502-503 | 2 | |
| β-strand | 505-506 | 2 | 4 |
| β-strand | 516 | 1 | 4 |
| β-strand | 523-528 | 6 | 5 |
| β-strand | 535-540 | 6 | 4 |
| α-helix | 541-543 | 3 | |
| β-strand | 550-556 | 7 | 5 |
| α-helix | 559 | 1 | |
| β-strand | 560 | 1 | 4 |
| α-helix | 561-562 | 2 | |
| β-strand | 569-575 | 7 | 4 |
| β-strand | 605-608 | 4 | 4 |
| α-helix | 610-612 | 3 | |
| α-helix | 613 | 1 | |
| β-strand | 614-616 | 3 | 5 |
| α-helix | 631-633 | 3 | |
| α-helix | 635-637 | 3 | |
| β-strand | 638-644 | 7 | 5 |
| α-helix | 645-648 | 4 | |
| β-strand | 653-658 | 6 | 4 |
| β-strand | 664-674 | 11 | 5 |
| α-helix | 675-678 | 4 | |
| β-strand | 679-681 | 3 | 6 |
| α-helix | 686-692 | 7 | |
| β-strand | 694-698 | 5 | 7 |
| α-helix | 699 | 1 | |
| β-strand | 705-710 | 6 | 6 |
| β-strand | 715 | 1 | 8 |
| β-strand | 719-724 | 6 | 7 |
| α-helix | 733-734 | 2 | |
| β-strand | 739-743 | 5 | 6 |
| β-strand | 750-754 | 5 | 6 |
| β-strand | 758-762 | 5 | 7 |
| β-strand | 766 | 1 | 8 |
| α-helix | 771-773 | 3 | |
| β-strand | 783-788 | 6 | 6 |
| β-strand | 797-803 | 7 | 7 |
| α-helix | 805-809 | 5 | |
| α-helix | 811-815 | 5 | |
| α-helix | 823-842 | 20 | |
| α-helix | 848-857 | 10 | |
| α-helix | 859-871 | 13 | |
| α-helix | 899-901 | 3 | |
| α-helix | 911-913 | 3 | |
| α-helix | 914-953 | 40 | |
| α-helix | 981-991 | 11 | |
| α-helix | 996-1021 | 26 | |
| α-helix | 1024-1041 | 18 | |
| α-helix | 1044-1047 | 4 | |
| α-helix | 1049-1058 | 10 | |
| α-helix | 1070-1073 | 4 | |
| α-helix | 1076-1083 | 8 | |
| α-helix | 1089-1093 | 5 | |
| α-helix | 1103-1123 | 21 | |
| α-helix | 1129-1132 | 4 | |
| α-helix | 1133-1149 | 17 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| GPI inositol-deacylase,fused thermostable green fluorescent protein | A | protein | 1469 | Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719), synthetic construct | G0S652 (AlphaFold model) |
>8K9Q_1 GPI inositol-deacylase,fused thermostable green fluorescent protein (chains A) MGSRSLSSASSDDDDAPPIRVPRVNQCATSRTKDSQSPAQSASKLDRRRSADRRPSFSAN RRSGTGAGTGTGTGIANWRPFDSRDATVERAGSSTATTATTPPPSSSLGLMLAANGAVQE KEMVMMGKAQEHGFVGRRAPWRSPWAISVFAFVTSLLGIGLLLAVIHSSVTRQIDPKGCR MSYMRPSYAKLSDFDTEHTRLASKYSLYLYREQGIDHDVKVRGVPVLFIPGNAGSYKQVR PIAAEAANYFHDVLQHDEAALRAGVRSLDFFTVDFNEDITAFHGQTLLDQAEYLNEAIRY ILSLYLDPRVSERDPDLPDPTSVIVLGHSMGGIVARTMLIMPNYQHNSINTIITMSAPHA RPPVSFDGQIVQTYKDINNYWRHAYSQKWANDNPLWHVTLVSIAGGGLDTVVPSDYASIE SLVPDTHGFTVFTSTIPNVWTSMDHQAILWCDQFRKVIIRALFDIVDVHRASQTKPRAQR MRVFKKWFLSGMETVAEKIAPTSDPTTLLIVDDKSDSITAEGERLVLRELGTQGSVRAHL MPIPPPGSPELKRFTLLTDTKLDKPGENGKLEVMFCSVIPSQPNPTGPAIPSQLDLSKGN AGTTRLACTNVAPDVITLPASTRFARFPFSVRKEAEIPPFSYLEYVLDDISEHQFVAVIE KATIPTPGFVIAEFSDHSNSHHTRHIGLRNLLTFGISLRLPSNRPMMSEVRIPSVKSSLL AYNLRISALECSGRKDLFAPLVRQYLAEPYESKYFVNARQAAVSLHGVAPYVPPPMSREP EAEGLAFQLWTDPTCNSSIQVDLTVDVMGSLGKLYMRYRTVFAAFPLFIVSLVLRKQFQV YDSTGSFITFAEGLDLSLRQSIPVMLIVLAALTLSTTKMAPSSSAGLWHWGGNTTFTNFH QNDLLIGTQDPFFLFLIPLIGIICVGVCTVVNYIALSLTRLISVVISFIGFLTVRFGWVN AEDRRRPSNPAIFPPSSPRRRMITTAVLLFLVSTMIPYQLAYLVACLVQLGTLVRAQRIS SELRSPANSNFHNYVHSIFILMLWILPINLPTLVVWMHNLSVHWLTPFTSHHNVFSIMPF ILLVETHTTGQMIPRTGGTGNGRCCVLLRHITSILLLSLALYAAVYGVSYAYTLHQFVNL FAFWLVMVHSTADDWSLTGLRQLILHNRNNANNKSETGSRKRGKEPGTLEVLFQGPGGSG GSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILT PAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEI RFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYK AKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGSAWSHPQFEKGGG SGGGSGGSAWSHPQFEKGSHHHHHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| D39 | (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-pr… | C40 H76 N O10 P | 2 |
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 3 |
Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis. Hong, J., Li, T., Chao, Y. et al. Nat Commun (2024) 15:8-8. DOI 10.1038/s41467-023-44568-2 · PubMed
Other PDB entries of the same protein (UniProt G0S652 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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