8K9R: GPI inositol-deacylase,MCherry protein

Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum. Determined by electron microscopy at 2.68 Å resolution. Released 20 Dec 2023.

Method
Electron microscopy
Resolution
2.68 Å
Organisms
Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719), Psychromonas sp. B3M02, synthetic construct
Chains
2
Atoms
7,684
Mol. weight
193.87 kDa
Ligands
80Y, CLR, PLM, L9H
Released
20 Dec 2023

Explore 8K9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K9R contains 49 α-helices and 40 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.

Chain A: 49 helices, 39 β-strands

ElementResiduesLengthSheet
α-helix147-16923
α-helix172-1743
β-strand17511
α-helix177-1793
β-strand18212
β-strand186-18833
α-helix198-2014
β-strand204-20853
β-strand21914
β-strand221-22773
α-helix234-2374
α-helix238-24710
α-helix248-2525
α-helix256-2605
β-strand265-27283
α-helix282-30221
β-strand30914
α-helix316-3183
β-strand321-32663
α-helix328-3369
α-helix342-3432
β-strand347-35373
α-helix366-38318
α-helix388-3903
β-strand397-40263
α-helix412-4154
β-strand426-43053
β-strand44011
α-helix445-4484
α-helix450-46112
β-strand46415
β-strand47215
α-helix475-48612
α-helix498-5003
α-helix502-5032
β-strand505-50956
β-strand51616
α-helix517-5182
β-strand523-52867
β-strand535-54066
α-helix541-5433
β-strand550-55677
α-helix559-5624
β-strand569-57686
α-helix577-5782
β-strand591-59446
β-strand602-60876
α-helix610-6123
α-helix6131
β-strand614-61637
α-helix631-6333
α-helix634-6374
β-strand638-64477
α-helix645-6484
β-strand653-65866
β-strand664-674117
α-helix675-6784
β-strand679-68138
α-helix686-6927
β-strand694-69859
β-strand705-71068
β-strand715110
β-strand719-72469
β-strand739-74468
β-strand74813
β-strand749-75468
β-strand758-76259
β-strand766110
α-helix771-7755
α-helix778-7803
β-strand783-78868
α-helix791-7933
β-strand797-80489
α-helix805-8106
α-helix812-8165
α-helix817-8215
α-helix824-84219
α-helix848-85710
α-helix859-87113
α-helix909-9135
α-helix914-95340
α-helix986-9927
α-helix996-102126
α-helix1024-106037
α-helix1068-108619
α-helix1089-10935
α-helix1103-112422
α-helix1131-114818
Chain B: 0 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand312

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
GPI inositol-deacylase,MCherry proteinAprotein1447Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719), Psychromonas sp. B3M02G0S652 (AlphaFold model)
Green fluorescent protein,Complement decay-accelerating factorBprotein272synthetic construct, Homo sapiensP08174 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8K9R_1 GPI inositol-deacylase,MCherry protein (chains A)
MGSRSLSSASSDDDDAPPIRVPRVNQCATSRTKDSQSPAQSASKLDRRRSADRRPSFSAN
RRSGTGAGTGTGTGIANWRPFDSRDATVERAGSSTATTATTPPPSSSLGLMLAANGAVQE
KEMVMMGKAQEHGFVGRRAPWRSPWAISVFAFVTSLLGIGLLLAVIHSSVTRQIDPKGCR
MSYMRPSYAKLSDFDTEHTRLASKYSLYLYREQGIDHDVKVRGVPVLFIPGNAGSYKQVR
PIAAEAANYFHDVLQHDEAALRAGVRSLDFFTVDFNEDITAFHGQTLLDQAEYLNEAIRY
ILSLYLDPRVSERDPDLPDPTSVIVLGHSMGGIVARTMLIMPNYQHNSINTIITMSAPHA
RPPVSFDGQIVQTYKDINNYWRHAYSQKWANDNPLWHVTLVSIAGGGLDTVVPSDYASIE
SLVPDTHGFTVFTSTIPNVWTSMDNQAILWCDQFRKVIIRALFDIVDVHRASQTKPRAQR
MRVFKKWFLSGMETVAEKIAPTSDPTTLLIVDDKSDSITAEGERLVLRELGTQGSVRAHL
MPIPPPGSPELKRFTLLTDTKLDKPGENGKLEVMFCSVIPSQPNPTGPAIPSQLDLSKGN
AGTTRLACTNVAPDVITLPASTRFARFPFSVRKEAEIPPFSYLEYVLDDISEHQFVAVIE
KATIPTPGFVIAEFSDHSNSHHTRHIGLRNLLTFGISLRLPSNRPMMSEVRIPSVKSSLL
AYNLRISALECSGRKDLFAPLVRQYLAEPYESKYFVNARQAAVSLHGVAPYVPPPMSREP
EAEGLAFQLWTDPTCNSSIQVDLTVDVMGSLGKLYMRYRTVFAAFPLFIVSLVLRKQFQV
YDSTGSFITFAEGLDLSLRQSIPVMLIVLAALTLSTTKMAPSSSAGLWHWGGNTTFTNFH
QNDLLIGTQDPFFLFLIPLIGIICVGVCTVVNYIALSLTRLISVVISFIGFLTVRFGWVN
AEDRRRPSNPAIFPPSSPRRRMITTAVLLFLVSTMIPYQLAYLVACLVQLGTLVRAQRIS
SELRSPANSNFHNYVHSIFILMLWILPINLPTLVVWMHNLSVHWLTPFTSHHNVFSIMPF
ILLVETHTTGQMIPRTGGTGNGRCCVLLRHITSILLLSLALYAAVYGVSYAYTLHQFVNL
FAFWLVMVHSTADDWSLTGLRQLILHNRNNANNKSETGSRKRGKEPGTLEVLFQGPKLEF
VSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPF
AWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDG
EFIYKVKLRGTNFPSDGPVMQKKTMGSEASSERMYPEDGALKGEVKYRLKLKDGGHYDAE
VKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYKSAHHH
HHHHHHH
Sequence of entity 2 (B), FASTA
>8K9R_2 Green fluorescent protein,Complement decay-accelerating factor (chains B)
GGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSY
DILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCF
FYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFK
TTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGSAWSHPQFE
KGGGSGGGSGGSAWSHPQFEKGSPNKGSGTTS

Ligands and cofactors

IDNameFormulaCopies
80Y2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl…C8 H18 N O9 P1
CLRCholesterolC27 H46 O1
PLMPalmitic acidC16 H32 O21
L9H[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis…C45 H89 O12 P1
PA12-amino-2-deoxy-alpha-D-glucopyranoseC6 H13 N O51
05E2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxi…C8 H18 N O9 P1
MANalpha-D-mannopyranoseC6 H12 O62

Primary citation

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:

Browse structure collections

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