8IMY: Cryo-EM structure of GPI-T (inactive mutant) with GPI and proULBP2, a proprotein substrate

PDB ID: 8IMYDownload
MMDB ID: 234268
PDB Deposition Date: 2023/3/7
Updated in MMDB: 2023/11
Experimental Method:
electron microscopy
Resolution: 3.22  Å
Source Organism:
synthetic construct▼
Similar Structures:
Biological Unit for 8IMY: hexameric; determined by author
Molecular Components in 8IMY
Label Count Molecule
Proteins (6 molecules)
1
Glycosylphosphatidylinositol Anchor Attachment 1 Protein,gfp-like Fluorescent Chromoprotein Cfp484
Molecule annotation
1
Gpi-anchor Transamidase,gfp-like Fluorescent Chromoprotein Cfp484
Molecule annotation
1
Phosphatidylinositol Glycan Anchor Biosynthesis Class U Protein,gfp-like Fluorescent Chromoprotein Cfp484
Molecule annotation
1
GPI Transamidase Component Pig-t,gfp-like Fluorescent Chromoprotein Cfp484
Molecule annotation
1
GPI Transamidase Component Pig-s,gfp-like Fluorescent Chromoprotein Cfp484
Molecule annotation
1
Ul16-binding Protein 2
Molecule annotation
Chemicals and Non-standard biopolymers (39 molecules)
1
4
2-acetamido-2-deoxy-beta-D-glucopyranose2-acetamido-2-deoxy-beta-D-glucopyranose
2
1
DigitoninDigitonin
3
6
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
4
19
CHOLESTEROL HEMISUCCINATECHOLESTEROL HEMISUCCINATE
5
1
MAGNESIUM IONMAGNESIUM ION
6
1
2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
7
2
2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate
8
1
CALCIUM IONCALCIUM ION
9
1
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
10
1
[(2R)-1-[[(1S,2R,3R,4S,5S,6R)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate[(2R)-1-[[(1S,2R,3R,4S,5S,6R)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate
11
1
2-amino-2-deoxy-alpha-D-glucopyranose2-amino-2-deoxy-alpha-D-glucopyranose
12
1
[(2R)-1-hexadecanoyloxy-3-[[3-[[(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (Z)-octadec-9-enoate[(2R)-1-hexadecanoyloxy-3-[[3-[[(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (Z)-octadec-9-enoate
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303