SMTL ID : 8imx.1

Cryo-EM structure of GPI-T with a chimeric GPI-anchored protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MET- SER- SER: Met-Ser-Ser peptide(Non-covalent)

MET-SER-SER.1: 9 residues within 4Å: Chain B: S.59 Chain C: R.62, C.208, D.233, S.234, L.235, S.236, H.246 Ligands: 80Y.27 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.62, C:D.233, C:S.234, C:S.236, C:H.246

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.2: 4 residues within 4Å: Chain B: N.205, M.209, Q.210, S.211 No protein-ligand interaction detected (PLIP)

13 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 5 residues within 4Å: Chain A: T.306, T.309 Ligands: 6OU.7, AJP.15, 81Q.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.309 Y01.5: 8 residues within 4Å: Chain B: L.398, H.399, L.429, A.499, L.502, V.503 Chain F: Y.351 Ligands: 6OU.20 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:L.429, B:A.499, B:L.502, B:V.503, F:Y.351 Y01.9: 7 residues within 4Å: Chain B: L.525, T.529, G.561, S.562, L.565 Ligands: Y01.10, Y01.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.529, B:L.565, B:L.565 Y01.10: 5 residues within 4Å: Chain B: L.286, Q.290, L.293, E.571 Ligands: Y01.9 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.286, B:L.293 Y01.11: 6 residues within 4Å: Chain B: L.552, A.557, G.561, L.574, L.576 Ligands: Y01.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.576 Y01.12: 8 residues within 4Å: Chain B: V.551, L.552, L.560, L.576, A.577, W.580 Ligands: Y01.13, Y01.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.551, B:L.552, B:A.577, B:W.580, B:W.580 Y01.13: 3 residues within 4Å: Chain B: L.478 Ligands: Y01.12, Y01.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.478 Y01.14: 6 residues within 4Å: Chain B: L.471, Y.474, A.475, L.478 Ligands: Y01.12, Y01.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.474, B:A.475 Y01.22: 7 residues within 4Å: Chain F: L.196, I.256, Y.260, G.261, L.264 Ligands: Y01.23, Y01.24 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.196, F:I.256, F:Y.260 Y01.23: 10 residues within 4Å: Chain F: L.196, L.199, L.264, S.265, S.288, L.289, V.292, Q.296, I.297 Ligands: Y01.22 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:L.196, F:L.199, F:L.264, F:L.264, F:V.292, F:Q.296, F:Q.296, F:I.297 Hydrogen bonds: F:S.265 Y01.24: 6 residues within 4Å: Chain F: L.239, V.240, I.243, W.253, I.256 Ligands: Y01.22 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.239, F:V.240, F:I.243, F:W.253, F:I.256, F:I.256 Y01.25: 4 residues within 4Å: Chain B: L.426 Chain F: F.145, T.361 Ligands: 6OU.20 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.145, F:T.361, B:L.426, B:L.426 Y01.26: 5 residues within 4Å: Chain F: L.78, Y.81, L.84, V.85, I.88 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.84, F:V.85, F:I.88

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: H.356, Q.357 Ligands: 05E.30 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.356

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

6OU.6: 23 residues within 4Å: Chain B: T.120, L.297, A.300, S.301, R.303, Y.474, L.522, L.526, P.555, T.558, L.559, S.562, L.563, W.566, L.582, A.585, A.586, L.587, Q.589, G.590, L.601, F.602, L.605 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.300, B:Y.474, B:L.522, B:L.526, B:T.558, B:L.559, B:L.559, B:L.559, B:L.563, B:L.563, B:W.566, B:W.566, B:F.602, B:L.605, B:L.605 Hydrogen bonds: B:R.303 Salt bridges: B:R.303 6OU.7: 15 residues within 4Å: Chain B: F.359, S.372, I.373, G.374, M.377, L.384, A.509, G.513, L.517 Chain F: V.366, L.370, F.388 Ligands: Y01.3, AJP.15, 81Q.31 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:L.384, B:A.509, B:L.517, B:L.517, F:L.370 Hydrogen bonds: B:S.372, B:G.374 6OU.8: 11 residues within 4Å: Chain B: R.313, Y.507, Q.511, C.514, L.600, L.604 Chain E: Y.363 Chain F: F.29, L.369, P.372, H.376 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:L.369, F:L.369, B:L.600 Salt bridges: F:H.376, F:H.376 6OU.20: 18 residues within 4Å: Chain B: W.395, L.433, I.506 Chain F: F.145, N.149, P.150, Y.151, F.344, N.348, Y.351, F.358, T.361, I.364, I.365, S.368, Y.407 Ligands: Y01.5, Y01.25 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:P.150, F:Y.151, F:F.358, F:F.358, F:I.364, F:I.365, B:L.433, B:I.506, B:I.506 Hydrogen bonds: F:N.348, F:N.348

1 x AJP: Digitonin(Non-covalent)

AJP.15: 13 residues within 4Å: Chain B: Q.48, Y.51, F.359, F.370, S.372, G.374, L.375, M.377, P.378, G.381, F.382 Ligands: Y01.3, 6OU.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.378, B:F.382 Hydrogen bonds: B:Q.48, B:Q.48, B:Y.51, B:S.372

1 x CA: CALCIUM ION(Non-covalent)

CA.16: 4 residues within 4Å: Chain C: D.81, I.84, E.120, D.122 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.81, C:I.84, C:E.120, C:D.122

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

NAG.17: 2 residues within 4Å: Chain D: N.269, Q.494 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.269 NAG.19: 6 residues within 4Å: Chain E: T.325, A.326, M.327, N.329, S.331, R.332 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.325, E:S.331

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

LBN.18: 24 residues within 4Å: Chain D: A.29, I.30, G.33, L.34, W.37, W.38, T.41, E.42, D.517, K.520, F.521, Y.524, I.525, F.528, M.531, A.532, I.535, L.536 Chain E: V.538 Chain F: F.290, V.294, I.297, N.298, F.301 19 PLIP interactions: 14 interactions with chain D, 4 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: D:I.30, D:W.37, D:W.37, D:W.37, D:F.521, D:Y.524, D:I.525, D:F.528, D:F.528, D:A.532, D:I.535, D:L.536, F:F.290, F:I.297, F:N.298, F:F.301, E:V.538 Hydrogen bonds: D:D.517 pi-Cation interactions: D:W.38

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.21: 19 residues within 4Å: Chain D: L.13, R.17, R.20, L.23, F.24, A.27, V.28 Chain F: F.202, L.206, L.207, V.217, K.218, M.219, F.224, W.225, S.228, W.229, A.307, K.311 19 PLIP interactions: 10 interactions with chain D, 9 interactions with chain F Hydrophobic interactions: D:L.23, D:L.23, D:F.24, D:A.27, D:V.28, F:F.202, F:L.206, F:L.207, F:W.225, F:W.229, F:K.311 Hydrogen bonds: D:R.20, F:M.219 Salt bridges: D:R.17, D:R.20, D:R.20, D:R.20, F:K.218, F:K.311

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.27: 7 residues within 4Å: Chain A: G.299, T.300, T.301 Ligands: MET-SER-SER.1, MET-SER-SER.1, 80Y.29, 05E.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.299, A:G.299, A:T.301, A:T.301 80Y.29: 9 residues within 4Å: Chain A: T.301 Chain B: Y.51, S.53, Q.357, S.358, F.359 Ligands: 80Y.27, PA1.28, 05E.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.51, B:S.53, B:Q.357, B:S.358

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

PA1.28: 6 residues within 4Å: Chain E: D.523, S.525 Chain F: N.385 Ligands: 80Y.29, 05E.30, 81Q.31 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.523, E:S.525

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.30: 10 residues within 4Å: Chain A: T.301 Chain B: H.356, Q.357 Chain C: D.176 Chain E: P.460, P.462 Ligands: MG.4, 80Y.27, PA1.28, 80Y.29 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.357, E:P.460 Salt bridges: B:H.356

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.31: 16 residues within 4Å: Chain A: L.310 Chain E: D.523, S.525, M.526, N.529 Chain F: V.359, C.362, I.363, V.366, N.387, F.388, A.391, T.395 Ligands: Y01.3, 6OU.7, PA1.28 7 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: F:V.359, F:V.366, A:L.310, A:L.310 Hydrogen bonds: F:N.387, E:S.525, E:N.529

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
G

C
K

D
S

E
T

F
U

Membrane

We predict this structure to be a membrane protein.
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UL16-binding protein 2,GFP-like fluorescent chromoprotein cFP484

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

GPI-anchor transamidase,GFP-like fluorescent chromoprotein cFP484

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

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

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

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