SMTL ID : 7wld.1

Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.53 Å

Oligo State

hetero-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: 5 residues within 4Å: Chain A: N.205, G.208, M.209, Q.210, S.211 No protein-ligand interaction detected (PLIP)

9 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 8 residues within 4Å: Chain A: L.525, T.529, T.558, G.561, S.562, L.565 Ligands: Y01.3, Y01.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.525, A:T.558 Y01.3: 4 residues within 4Å: Chain A: L.286, L.293, L.565 Ligands: Y01.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.286, A:L.293, A:L.565 Y01.8: 6 residues within 4Å: Chain A: V.551, L.552, A.557, L.560, L.576, W.580 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.551, A:L.552, A:A.557, A:L.560, A:L.576, A:W.580, A:W.580 Y01.9: 5 residues within 4Å: Chain A: L.552, A.557, G.561, F.564 Ligands: Y01.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.564 Y01.10: 5 residues within 4Å: Chain A: L.398, H.399, V.503 Chain E: Y.351 Ligands: DKB.24 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.398, A:L.398, A:V.503, E:Y.351 Y01.21: 8 residues within 4Å: Chain E: L.196, L.239, I.256, P.257, Y.260, G.261 Ligands: Y01.25, Y01.26 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.196, E:L.239, E:I.256, E:Y.260 Y01.25: 9 residues within 4Å: Chain E: L.264, L.289, V.292, C.293, Q.296, I.297, F.300 Ligands: CLR.15, Y01.21 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.264, E:L.264, E:L.264, E:L.289, E:V.292, E:V.292, E:Q.296, E:I.297, E:F.300, E:F.300 Y01.26: 3 residues within 4Å: Chain E: V.240, I.256 Ligands: Y01.21 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.240, E:I.256 Y01.27: 3 residues within 4Å: Chain E: K.222, W.225 Ligands: CDL.20 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.225, E:W.225, E:W.225, E:W.225 Salt bridges: E:K.222

1 x AJP: Digitonin(Non-covalent)

AJP.4: 10 residues within 4Å: Chain A: Q.48, Y.51, F.359, F.370, S.372, G.374, M.377, P.378, G.381 Ligands: BJR.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.378 Hydrogen bonds: A:Q.48, A:Y.51, A:S.372, A:S.372

2 x BJR: (4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium(Non-covalent)

BJR.5: 11 residues within 4Å: Chain A: Q.511, C.514, T.518, L.600, L.604, L.607, G.608 Chain E: F.29, P.372, V.373, H.376 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:Q.511, A:T.518, A:L.604, A:L.607, E:P.372 Salt bridges: E:H.376, E:H.376, E:H.376 pi-Cation interactions: E:F.29 BJR.6: 13 residues within 4Å: Chain A: S.358, F.359, S.372, I.373, G.374, M.377, L.384, A.509, G.513 Chain E: F.388 Ligands: AJP.4, PA1.19, 06O.28 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.384, A:L.384, A:A.509 Hydrogen bonds: A:S.372, A:G.374

1 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.7: 22 residues within 4Å: Chain A: L.297, R.298, S.301, R.303, L.443, L.470, L.471, Y.474, L.522, P.555, T.558, L.559, S.562, L.563, W.566, L.582, A.585, A.586, L.587, Q.589, L.601, F.602 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:R.298, A:L.443, A:L.471, A:Y.474, A:Y.474, A:L.522, A:T.558, A:L.559, A:L.559, A:L.563, A:W.566, A:W.566, A:L.587, A:F.602 Hydrogen bonds: A:L.582 Salt bridges: A:R.303, A:R.303

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 3 residues within 4Å: Chain B: D.81, I.84, D.122 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.81, B:I.84, B:D.122, B:D.122

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.12: 10 residues within 4Å: Chain B: V.383, T.387, Y.388 Chain E: F.171, T.175, K.178, S.180, L.183 Ligands: CLR.22, CLR.23 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:V.383, B:Y.388, E:F.171, E:F.171 Hydrogen bonds: B:T.387, B:Y.388

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

NAG.13: 2 residues within 4Å: Chain C: L.227, N.269 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.227 NAG.18: 1 residues within 4Å: Chain D: N.329 No protein-ligand interaction detected (PLIP)

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.14: 10 residues within 4Å: Chain C: G.33, W.37, Y.524, L.527, F.528 Chain E: F.290, V.294, I.297, N.298, F.301 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain E Hydrophobic interactions: C:W.37, C:Y.524, C:F.528, E:F.290, E:V.294, E:I.297, E:N.298, E:F.301 Hydrogen bonds: C:W.37 CLR.15: 6 residues within 4Å: Chain C: L.36, K.39, T.40 Chain E: L.289, C.293 Ligands: Y01.25 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:T.40, E:L.289, E:L.289 CLR.16: 5 residues within 4Å: Chain C: R.20, L.23, F.24, A.27 Ligands: CDL.20 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:R.20, C:L.23, C:L.23, C:F.24, C:F.24, C:A.27 CLR.22: 9 residues within 4Å: Chain B: L.379, V.383 Chain E: I.186, L.190, M.234, G.237, S.238, V.241 Ligands: P5S.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:L.379, B:L.379, B:V.383, E:L.190, E:V.241 CLR.23: 6 residues within 4Å: Chain E: L.92, F.99, F.171, L.174, K.178 Ligands: P5S.12 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.99, E:F.99, E:F.99, E:F.171, E:L.174, E:K.178

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.17: 4 residues within 4Å: Chain A: H.356 Chain D: N.463, F.524 Ligands: PA1.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.463

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

PA1.19: 4 residues within 4Å: Chain D: D.523 Ligands: BJR.6, 05E.17, 06O.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.523

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.20: 15 residues within 4Å: Chain C: R.17, R.20 Chain E: F.202, V.203, L.206, V.217, K.218, M.219, S.228, W.229, I.304, A.307, K.311 Ligands: CLR.16, Y01.27 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:F.202, E:V.203, E:V.203, E:L.206, E:W.229, E:I.304, E:I.304 Hydrogen bonds: E:M.219 Salt bridges: E:K.218, E:K.311, E:K.311, C:R.17, C:R.20

1 x DKB: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate(Non-covalent)

DKB.24: 17 residues within 4Å: Chain A: V.503, I.506, Y.507, L.510 Chain E: N.149, P.150, Y.151, M.341, F.344, N.348, Y.351, F.358, T.361, S.368, L.369, Y.407 Ligands: Y01.10 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain E Hydrophobic interactions: A:I.506, A:Y.507, A:Y.507, E:P.150, E:Y.151, E:Y.151, E:F.344, E:F.358, E:T.361 Hydrogen bonds: E:N.348

1 x 06O: [(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{Z},11~{Z})-octadeca-9,11-dienoate(Non-covalent)

06O.28: 12 residues within 4Å: Chain D: D.523, S.525 Chain E: I.363, N.385, N.387, F.388, A.391, I.392, L.394, T.395 Ligands: BJR.6, PA1.19 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:I.363, E:N.387, E:F.388, E:A.391, E:L.394 Hydrogen bonds: E:N.385, E:N.387, D:S.525, D:S.525

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Molecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins. Nat Commun (2022)

Release Date

2022-04-27

Peptides

Glycosylphosphatidylinositol anchor attachment 1 protein: A
GPI-anchor transamidase: B
GPI transamidase component PIG-S: C
GPI transamidase component PIG-T: D
Phosphatidylinositol glycan anchor biosynthesis class U protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
K

C
S

D
T

E
U

Membrane

We predict this structure to be a membrane protein.
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Glycosylphosphatidylinositol anchor attachment 1 protein

GPI-anchor transamidase

GPI transamidase component PIG-S

GPI transamidase component PIG-T

Phosphatidylinositol glycan anchor biosynthesis class U protein

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