SMTL ID : 8imy.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.205, G.208, M.209, Q.210 No protein-ligand interaction detected (PLIP)

1 x AJP: Digitonin(Non-covalent)

AJP.2: 14 residues within 4Å: Chain A: Q.48, Y.51, F.359, F.370, S.372, G.374, L.375, P.378, G.381, F.382 Ligands: 6OU.4, 80Y.16, Y01.37, 80Y.38 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.378, A:F.382 Hydrogen bonds: A:Q.48, A:Y.51

6 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.3: 23 residues within 4Å: Chain A: L.297, R.298, A.300, S.301, R.303, H.305, Y.474, L.522, L.526, P.555, T.558, L.559, S.562, L.563, W.566, A.585, A.586, L.587, Q.589, G.590, L.601, F.602, L.605 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.300, A:Y.474, A:L.522, A:L.526, A:T.558, A:L.559, A:L.563, A:W.566, A:W.566, A:W.566, A:L.587, A:L.601, A:F.602, A:L.605 Salt bridges: A:R.303, A:R.303, A:R.303 6OU.4: 15 residues within 4Å: Chain A: F.359, S.372, I.373, G.374, M.377, L.384, G.388, A.509, G.513 Chain C: V.366, L.370, F.388 Ligands: AJP.2, 81Q.30, Y01.37 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.384, C:V.366, C:L.370 Hydrogen bonds: A:S.372, A:G.374 6OU.5: 12 residues within 4Å: Chain A: N.245, R.313, Q.511, C.514, T.518, L.600, L.604 Chain C: F.29, P.372, H.376 Chain D: Y.363 Ligands: 6OU.27 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.600, A:L.604, C:P.372 Hydrogen bonds: A:N.245, A:R.313, C:H.376 Salt bridges: C:H.376, C:H.376 6OU.18: 17 residues within 4Å: Chain B: L.376, I.380, M.382, V.383, K.386 Chain C: L.70, F.182, I.186, L.190, W.229, E.230, M.233, M.234, G.237, S.238, V.241, I.242 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:L.376, B:I.380, B:M.382, B:V.383, C:L.70, C:F.182, C:F.182, C:I.186, C:I.186, C:L.190, C:V.241, C:V.241, C:I.242 6OU.27: 18 residues within 4Å: Chain A: V.503, Y.507 Chain C: K.141, P.150, Y.151, M.341, F.344, N.348, Y.351, I.357, F.358, T.361, S.368, L.369, Y.407 Ligands: 6OU.5, Y01.12, Y01.13 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.150, C:Y.151, C:Y.151, C:F.344, C:F.344, C:F.358, C:T.361, C:L.369, A:V.503 Hydrogen bonds: C:N.348, C:N.348 Salt bridges: C:K.141 6OU.34: 5 residues within 4Å: Chain C: C.293 Chain E: L.32, P.35, K.39, T.40 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.32

19 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 6 residues within 4Å: Chain A: T.529, G.561, L.565, E.568 Ligands: Y01.7, Y01.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.529, A:L.565, A:E.568 Y01.7: 4 residues within 4Å: Chain A: L.286, Q.290, L.293 Ligands: Y01.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.286, A:L.293 Y01.8: 4 residues within 4Å: Chain A: L.552, G.561, F.564 Ligands: Y01.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.564 Y01.9: 8 residues within 4Å: Chain A: L.552, A.557, L.560, L.576, W.580, Q.581 Ligands: Y01.10, Y01.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.552, A:A.557, A:L.576, A:L.576, A:W.580, A:W.580 Y01.10: 3 residues within 4Å: Chain A: L.478 Ligands: Y01.9, Y01.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.478 Y01.11: 8 residues within 4Å: Chain A: L.471, Y.474, A.475, L.478, V.551, W.580 Ligands: Y01.9, Y01.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.471, A:L.471, A:Y.474, A:Y.474, A:L.478, A:V.551, A:W.580 Y01.12: 6 residues within 4Å: Chain A: W.395, L.398, H.399 Chain C: Y.351 Ligands: Y01.13, 6OU.27 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.395, A:L.398, C:Y.351 Y01.13: 6 residues within 4Å: Chain A: L.426 Chain C: F.145, T.361, I.365 Ligands: Y01.12, 6OU.27 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.145, C:T.361, C:I.365 Y01.19: 7 residues within 4Å: Chain C: L.196, L.239, I.256, Y.260, G.261, L.264 Ligands: Y01.20 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.196, C:L.239, C:I.256, C:Y.260, C:Y.260, C:L.264 Y01.20: 11 residues within 4Å: Chain C: L.264, S.265, S.288, L.289, V.292, C.293, Q.296, I.297, F.300 Ligands: Y01.19, 80T.32 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.264, C:L.264, C:L.289, C:V.292, C:Q.296, C:Q.296, C:I.297, C:F.300, C:F.300 Hydrogen bonds: C:S.265 Y01.21: 4 residues within 4Å: Chain C: V.240, W.253, D.254, I.256 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.240, C:W.253, C:I.256, C:I.256 Hydrogen bonds: C:D.254 Y01.22: 5 residues within 4Å: Chain C: M.219, K.220, K.222, W.225 Ligands: 80T.32 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.222, C:W.225 Y01.23: 6 residues within 4Å: Chain C: T.16, A.19, R.23, D.80, Y.81, L.84 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.81 Hydrogen bonds: C:D.80, C:D.80 Y01.24: 4 residues within 4Å: Chain C: L.92, I.95, F.99, K.178 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.92, C:I.95, C:F.99, C:F.99 Salt bridges: C:K.178 Y01.25: 9 residues within 4Å: Chain C: L.74, L.78, V.85, I.88, T.89, L.92, T.167, F.171, F.187 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.74, C:L.78, C:L.78, C:V.85, C:V.85, C:I.88, C:I.88, C:T.89, C:L.92, C:T.167, C:F.171, C:F.187 Y01.26: 6 residues within 4Å: Chain B: G.371, F.372 Chain C: V.241, C.244, L.245, F.248 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.241, C:V.241, C:L.245, C:F.248, C:F.248 Y01.35: 8 residues within 4Å: Chain E: K.19, R.20, L.23, F.24, A.27, V.28, V.31 Ligands: 80T.32 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:K.19, E:L.23, E:F.24, E:V.28, E:V.31 Salt bridges: E:K.19, E:R.20 Y01.36: 7 residues within 4Å: Chain E: D.518, F.521 Chain F: T.239, I.242, L.243, L.246, L.250 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:T.239, F:I.242, F:L.246, F:L.250, E:F.521, E:F.521 Y01.37: 6 residues within 4Å: Chain F: A.238, T.240, C.244 Ligands: AJP.2, 6OU.4, 81Q.30 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 3 residues within 4Å: Chain A: H.356, Q.357 Ligands: 05E.15 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.356

1 x 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(Non-covalent)

05E.15: 10 residues within 4Å: Chain A: H.356, Q.357 Chain B: D.176 Chain D: P.462, D.523, F.524, S.525 Ligands: MG.14, 80Y.16, PA1.31 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:D.523, D:F.524, A:Q.357 Salt bridges: A:H.356

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

80Y.16: 10 residues within 4Å: Chain A: Y.51, S.53, Q.357, S.358, F.359 Chain F: T.232 Ligands: AJP.2, 05E.15, PA1.31, 80Y.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.51, A:S.53, A:S.358 80Y.38: 6 residues within 4Å: Chain A: S.53, N.55 Chain F: T.231, T.232 Ligands: AJP.2, 80Y.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.53, A:N.55

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 4 residues within 4Å: Chain B: D.81, I.84, E.120, D.122 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.81, B:I.84, B:E.120, B:D.122, B:D.122

1 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.28: 16 residues within 4Å: Chain C: V.294, I.297, N.298, F.301 Chain E: I.30, G.33, W.37, W.38, T.41, K.520, F.521, Y.524, I.525, F.528, M.531, A.532 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:I.30, E:W.37, E:W.37, E:Y.524, E:I.525, E:F.528, E:F.528, E:F.528, E:A.532, C:I.297, C:F.301 Hydrogen bonds: E:D.517, E:Y.524 Salt bridges: E:K.520 pi-Cation interactions: E:W.38

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.29: 3 residues within 4Å: Chain D: T.325, A.326, N.329 No protein-ligand interaction detected (PLIP) NAG.33: 3 residues within 4Å: Chain E: L.227, N.269, Q.494 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.227

1 x 81Q: [(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(Non-covalent)

81Q.30: 20 residues within 4Å: Chain A: L.392 Chain C: F.358, V.359, C.362, I.363, V.366, N.385, N.387, F.388, A.391, T.395 Chain D: D.523, S.525, M.526, N.529, L.533 Chain F: L.241 Ligands: 6OU.4, PA1.31, Y01.37 17 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D, 2 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: C:F.358, C:V.359, C:I.363, C:V.366, C:N.387, C:F.388, C:A.391, D:L.533, F:L.241, F:L.241, A:L.392 Hydrogen bonds: C:N.385, C:N.387, D:D.523, D:S.525, D:S.525, D:N.529

1 x PA1: 2-amino-2-deoxy-alpha-D-glucopyranose(Non-covalent)

PA1.31: 6 residues within 4Å: Chain C: N.385 Chain D: D.523, S.525 Ligands: 05E.15, 80Y.16, 81Q.30 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.523, D:D.523, D:S.525

1 x 80T: [(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(Non-covalent)

80T.32: 20 residues within 4Å: Chain C: F.202, V.203, L.206, L.207, V.217, K.218, M.219, F.224, W.225, S.228, W.229, I.304, A.307, I.308, K.311 Chain E: R.17, R.20 Ligands: Y01.20, Y01.22, Y01.35 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:F.202, C:V.203, C:L.206, C:F.224, C:W.225, C:W.225, C:W.225, C:W.229, C:I.304, C:I.304, C:K.311 Hydrogen bonds: C:M.219 Salt bridges: C:K.311, C:K.311, E:R.17, E:R.20, E:R.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Nat Commun (2023)

Release Date

2023-08-16

Peptides

Glycosylphosphatidylinositol anchor attachment 1 protein,GFP-like fluorescent chromoprotein cFP484: A
GPI-anchor transamidase,GFP-like fluorescent chromoprotein cFP484: B
Phosphatidylinositol glycan anchor biosynthesis class U protein,GFP-like fluorescent chromoprotein cFP484: C
GPI transamidase component PIG-T,GFP-like fluorescent chromoprotein cFP484: D
GPI transamidase component PIG-S,GFP-like fluorescent chromoprotein cFP484: E
UL16-binding protein 2: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
K

C
U

D
T

E
S

F
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Glycosylphosphatidylinositol anchor attachment 1 protein,GFP-like fluorescent chromoprotein cFP484

GPI-anchor transamidase,GFP-like fluorescent chromoprotein cFP484

Phosphatidylinositol glycan anchor biosynthesis class U protein,GFP-like fluorescent chromoprotein cFP484

GPI transamidase component PIG-T,GFP-like fluorescent chromoprotein cFP484

GPI transamidase component PIG-S,GFP-like fluorescent chromoprotein cFP484

UL16-binding protein 2

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