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- EMDB-36997: Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Ch... -

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Entry
Database: EMDB / ID: EMD-36997
TitleCryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
Map data
Sample
  • Complex: Complex of PGAP1 with a chimera GPI-anchored protein
    • Protein or peptide: GPI inositol-deacylase,MCherry protein
  • Protein or peptide: Green fluorescent protein,Complement decay-accelerating factor
  • Ligand: PALMITIC ACID
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
  • Ligand: 2-amino-2-deoxy-alpha-D-glucopyranose
  • Ligand: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate
  • Ligand: CHOLESTEROL
  • Ligand: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate
KeywordsBst1 / Glycosylphosphatidylinositol / GPI anchoring / GPI-AP / GPI-AP remodelase / Integral membrane enzyme / Lipase / Lipid remodeling / Membrane enzyme / Membrane protein / Nanodisc / PGAP1 / TGP / Thermostable green fluorescence protein / Transmembrane enzyme / Triad enzyme.
Function / homology
Function and homology information


GPI anchor metabolic process / phosphatidylinositol deacylase activity / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) ...GPI anchor metabolic process / phosphatidylinositol deacylase activity / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / side of membrane / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / bioluminescence / generation of precursor metabolites and energy / positive regulation of T cell cytokine production / protein transport / positive regulation of cytosolic calcium ion concentration / virus receptor activity / Hydrolases; Acting on ester bonds / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
GPI inositol-deacylase / : / GPI inositol-deacylase transmembrane domain / GPI inositol-deacylase beta-sandwich domain / GPI inositol-deacylase PGAP1-like / PGAP1-like alpha/beta domain / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...GPI inositol-deacylase / : / GPI inositol-deacylase transmembrane domain / GPI inositol-deacylase beta-sandwich domain / GPI inositol-deacylase PGAP1-like / PGAP1-like alpha/beta domain / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Uncharacterized protein / GPI inositol-deacylase / Complement decay-accelerating factor
Similarity search - Component
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Psychromonas sp. B3M02 (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsLi T / Hong J / Qu Q / Li D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82151215 China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.
Authors: Jingjing Hong / Tingting Li / Yulin Chao / Yidan Xu / Zhini Zhu / Zixuan Zhou / Weijie Gu / Qianhui Qu / Dianfan Li /
Abstract: The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates ...The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates the inositol in nascent GPI-APs. Impairment of PGAP1 activity leads to developmental diseases in humans and fatality and infertility in animals. Here, we present three PGAP1 structures (2.66-2.84 Å), revealing its 10-transmembrane architecture and product-enzyme interaction details. PGAP1 holds GPI-AP acyl chains in an optimally organized, guitar-shaped cavity with apparent energetic penalties from hydrophobic-hydrophilic mismatches. However, abundant glycan-mediated interactions in the lumen counterbalance these repulsions, likely conferring substrate fidelity and preventing off-target hydrolysis of bulk membrane lipids. Structural and biochemical analyses uncover a serine hydrolase-type catalysis with atypical features and imply mechanisms for substrate entrance and product release involving a drawing compass movement of GPI-APs. Our findings advance the mechanistic understanding of GPI-AP remodeling.
History
DepositionAug 1, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36997.png

Downloads & links

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Map

FileDownload / File: emd_36997.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 270 pix.
= 251.64 Å		0.93 Å/pix.
x 270 pix.
= 251.64 Å		0.93 Å/pix.
x 270 pix.
= 251.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.546
Minimum - Maximum-2.5902214 - 3.9916897
Average (Standard dev.)0.00007376662 (±0.1074597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 251.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36997_additional_1.map
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Half map: #1

Fileemd_36997_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_36997_half_map_2.map
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Sample components

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Entire : Complex of PGAP1 with a chimera GPI-anchored protein

EntireName: Complex of PGAP1 with a chimera GPI-anchored protein
Components
  • Complex: Complex of PGAP1 with a chimera GPI-anchored protein
    • Protein or peptide: GPI inositol-deacylase,MCherry protein
  • Protein or peptide: Green fluorescent protein,Complement decay-accelerating factor
  • Ligand: PALMITIC ACID
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
  • Ligand: 2-amino-2-deoxy-alpha-D-glucopyranose
  • Ligand: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate
  • Ligand: CHOLESTEROL
  • Ligand: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate

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Supramolecule #1: Complex of PGAP1 with a chimera GPI-anchored protein

SupramoleculeName: Complex of PGAP1 with a chimera GPI-anchored protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 194 KDa

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Macromolecule #1: GPI inositol-deacylase,MCherry protein

MacromoleculeName: GPI inositol-deacylase,MCherry protein / type: protein_or_peptide / ID: 1
Details: Residues 1-1186 is GPI inositol-deacylase (Uniprot ID G0S652) with a S327A mutation. Residues 1187-1200 is the linker with a 3 C protease digestion site. Residues 1201-1435 is a fused ...Details: Residues 1-1186 is GPI inositol-deacylase (Uniprot ID G0S652) with a S327A mutation. Residues 1187-1200 is the linker with a 3 C protease digestion site. Residues 1201-1435 is a fused mCherry protein (Uniprot ID A0A366VY15 with the following four mutations that extend its fluorescence lifetime: W148S, I166V, Q168Y and I202R). Residues 1436-1447 is the linker with a His tag.
Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Psychromonas sp. B3M02 (bacteria)
Molecular weightTheoretical: 161.345547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSRSLSSAS SDDDDAPPIR VPRVNQCATS RTKDSQSPAQ SASKLDRRRS ADRRPSFSAN RRSGTGAGTG TGTGIANWRP FDSRDATVE RAGSSTATTA TTPPPSSSLG LMLAANGAVQ EKEMVMMGKA QEHGFVGRRA PWRSPWAISV FAFVTSLLGI G LLLAVIHS ...String:
MGSRSLSSAS SDDDDAPPIR VPRVNQCATS RTKDSQSPAQ SASKLDRRRS ADRRPSFSAN RRSGTGAGTG TGTGIANWRP FDSRDATVE RAGSSTATTA TTPPPSSSLG LMLAANGAVQ EKEMVMMGKA QEHGFVGRRA PWRSPWAISV FAFVTSLLGI G LLLAVIHS SVTRQIDPKG CRMSYMRPSY AKLSDFDTEH TRLASKYSLY LYREQGIDHD VKVRGVPVLF IPGNAGSYKQ VR PIAAEAA NYFHDVLQHD EAALRAGVRS LDFFTVDFNE DITAFHGQTL LDQAEYLNEA IRYILSLYLD PRVSERDPDL PDP TSVIVL GHAMGGIVAR TMLIMPNYQH NSINTIITMS APHARPPVSF DGQIVQTYKD INNYWRHAYS QKWANDNPLW HVTL VSIAG GGLDTVVPSD YASIESLVPD THGFTVFTST IPNVWTSMDH QAILWCDQFR KVIIRALFDI VDVHRASQTK PRAQR MRVF KKWFLSGMET VAEKIAPTSD PTTLLIVDDK SDSITAEGER LVLRELGTQG SVRAHLMPIP PPGSPELKRF TLLTDT KLD KPGENGKLEV MFCSVIPSQP NPTGPAIPSQ LDLSKGNAGT TRLACTNVAP DVITLPASTR FARFPFSVRK EAEIPPF SY LEYVLDDISE HQFVAVIEKA TIPTPGFVIA EFSDHSNSHH TRHIGLRNLL TFGISLRLPS NRPMMSEVRI PSVKSSLL A YNLRISALEC SGRKDLFAPL VRQYLAEPYE SKYFVNARQA AVSLHGVAPY VPPPMSREPE AEGLAFQLWT DPTCNSSIQ VDLTVDVMGS LGKLYMRYRT VFAAFPLFIV SLVLRKQFQV YDSTGSFITF AEGLDLSLRQ SIPVMLIVLA ALTLSTTKMA PSSSAGLWH WGGNTTFTNF HQNDLLIGTQ DPFFLFLIPL IGIICVGVCT VVNYIALSLT RLISVVISFI GFLTVRFGWV N AEDRRRPS NPAIFPPSSP RRRMITTAVL LFLVSTMIPY QLAYLVACLV QLGTLVRAQR ISSELRSPAN SNFHNYVHSI FI LMLWILP INLPTLVVWM HNLSVHWLTP FTSHHNVFSI MPFILLVETH TTGQMIPRTG GTGNGRCCVL LRHITSILLL SLA LYAAVY GVSYAYTLHQ FVNLFAFWLV MVHSTADDWS LTGLRQLILH NRNNANNKSE TGSRKRGKEP GTLEVLFQGP KLEF VSKGE EDNMAIIKEF MRFKVHMEGS VNGHEFEIEG EGEGRPYEGT QTAKLKVTKG GPLPFAWDIL SPQFMYGSKA YVKHP ADIP DYLKLSFPEG FKWERVMNFE DGGVVTVTQD SSLQDGEFIY KVKLRGTNFP SDGPVMQKKT MGSEASSERM YPEDGA LKG EVKYRLKLKD GGHYDAEVKT TYKAKKPVQL PGAYNVNRKL DITSHNEDYT IVEQYERAEG RHSTGGMDEL YKSAHHH HH HHHHH

UniProtKB: GPI inositol-deacylase, Uncharacterized protein

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Macromolecule #2: Green fluorescent protein,Complement decay-accelerating factor

MacromoleculeName: Green fluorescent protein,Complement decay-accelerating factor
type: protein_or_peptide / ID: 2
Details: Residues 1-6 is a linker. Residues 7-231 is a thermostable green fluorescent protein (PDB entry 4TZA, residue 5-229). Residues 232-263 is a linker with an expression tag. Residues 264-272 is ...Details: Residues 1-6 is a linker. Residues 7-231 is a thermostable green fluorescent protein (PDB entry 4TZA, residue 5-229). Residues 232-263 is a linker with an expression tag. Residues 264-272 is human CD55 (Uniprot ID P08174, residue P345-S353)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.894154 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGSGGSASVI KPEMKIKLRM EGAVNGHKFV IEGEGIGKPY EGTQTLDLTV EEGAPLPFSY DILTPAFQYG NRAFTKYPED IPDYFKQAF PEGYSWERSM TYEDQGICIA TSDITMEGDC FFYEIRFDGT NFPPNGPVMQ KKTLKWEPST EKMYVEDGVL K GDVEMALL ...String:
GGSGGSASVI KPEMKIKLRM EGAVNGHKFV IEGEGIGKPY EGTQTLDLTV EEGAPLPFSY DILTPAFQYG NRAFTKYPED IPDYFKQAF PEGYSWERSM TYEDQGICIA TSDITMEGDC FFYEIRFDGT NFPPNGPVMQ KKTLKWEPST EKMYVEDGVL K GDVEMALL LEGGGHYRCD FKTTYKAKKD VRLPDAHEVD HRIEILSHDK DYNKVRLYEH AEARYSGGGS GGGSAWSHPQ FE KGGGSGG GSGGSAWSHP QFEKGSPNKG SGTTS

UniProtKB: Complement decay-accelerating factor

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #5: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-...

MacromoleculeName: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
type: ligand / ID: 5 / Number of copies: 1 / Formula: 05E
Molecular weightTheoretical: 303.204 Da
Chemical component information

ChemComp-05E:
2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate

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Macromolecule #6: 2-amino-2-deoxy-alpha-D-glucopyranose

MacromoleculeName: 2-amino-2-deoxy-alpha-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: PA1
Molecular weightTheoretical: 179.171 Da
Chemical component information

ChemComp-PA1:
2-amino-2-deoxy-alpha-D-glucopyranose

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Macromolecule #7: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,...

MacromoleculeName: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate
type: ligand / ID: 7 / Number of copies: 1 / Formula: LYI
Molecular weightTheoretical: 873.144 Da
Chemical component information

ChemComp-LYI:
[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate

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Macromolecule #8: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #9: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-...

MacromoleculeName: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate
type: ligand / ID: 9 / Number of copies: 1 / Formula: 80Y
Molecular weightTheoretical: 303.204 Da
Chemical component information

ChemComp-80Y:
2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration14.9 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
0.008 %GDNglyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 353585
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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