SMTL ID : 5szs.1

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 9 residues within 4Å: Chain A: L.223, T.224, N.225, Y.237, R.365, T.366, Q.368, Y.370, F.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.237, A:Q.368 NAG-NAG-BMA-MAN-MAN-MAN.22: 9 residues within 4Å: Chain B: L.223, T.224, N.225, Y.237, R.365, T.366, Q.368, Y.370, F.405 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.237, B:Q.368 NAG-NAG-BMA-MAN-MAN-MAN.43: 9 residues within 4Å: Chain C: L.223, T.224, N.225, Y.237, R.365, T.366, Q.368, Y.370, F.405 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.237, C:Q.368

33 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: 3 residues within 4Å: Chain A: Y.259, N.261, T.263 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.315, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: I.342, N.343, G.519, S.520 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: F.257, V.299, V.301, N.386, N.388 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: T.475, A.476, S.477, Q.489, N.491 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain A: N.708 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: R.731, P.732, N.734 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain A: A.746, N.747 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain A: N.753, E.955, D.1122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.955 NAG-NAG.17: 3 residues within 4Å: Chain A: N.829, V.830, R.845 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain A: I.743, S.1130, N.1181, V.1182, T.1183 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain B: Y.259, N.261, T.263 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain B: N.315, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain B: I.342, N.343, G.519, S.520 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain B: F.257, V.299, V.301, N.386, N.388 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain B: T.475, A.476, S.477, Q.489, N.491 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 1 residues within 4Å: Chain B: N.708 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain B: R.731, P.732, N.734 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain B: A.746, N.747 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain B: N.753, E.955, D.1122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.955 NAG-NAG.38: 3 residues within 4Å: Chain B: N.829, V.830, R.845 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 5 residues within 4Å: Chain B: I.743, S.1130, N.1181, V.1182, T.1183 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 3 residues within 4Å: Chain C: Y.259, N.261, T.263 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 2 residues within 4Å: Chain C: N.315, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 4 residues within 4Å: Chain C: I.342, N.343, G.519, S.520 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 5 residues within 4Å: Chain C: F.257, V.299, V.301, N.386, N.388 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 5 residues within 4Å: Chain C: T.475, A.476, S.477, Q.489, N.491 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 1 residues within 4Å: Chain C: N.708 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 3 residues within 4Å: Chain C: R.731, P.732, N.734 No protein-ligand interaction detected (PLIP) NAG-NAG.57: 2 residues within 4Å: Chain C: A.746, N.747 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 3 residues within 4Å: Chain C: N.753, E.955, D.1122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.955 NAG-NAG.59: 3 residues within 4Å: Chain C: N.829, V.830, R.845 No protein-ligand interaction detected (PLIP) NAG-NAG.62: 5 residues within 4Å: Chain C: I.743, S.1130, N.1181, V.1182, T.1183 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain A: V.248, N.286, S.288, T.395, F.397, W.398 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 4 residues within 4Å: Chain A: G.834, N.837, S.839, N.969 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 6 residues within 4Å: Chain B: V.248, N.286, S.288, T.395, F.397, W.398 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.39: 4 residues within 4Å: Chain B: G.834, N.837, S.839, N.969 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.45: 6 residues within 4Å: Chain C: V.248, N.286, S.288, T.395, F.397, W.398 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.60: 4 residues within 4Å: Chain C: G.834, N.837, S.839, N.969 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.5: 6 residues within 4Å: Chain A: L.310, Y.312, V.320, T.323, N.339, S.348 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 6 residues within 4Å: Chain B: L.310, Y.312, V.320, T.323, N.339, S.348 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.47: 6 residues within 4Å: Chain C: L.310, Y.312, V.320, T.323, N.339, S.348 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.8: 13 residues within 4Å: Chain A: E.132, Y.151, K.152, N.411, S.413, N.419, F.437, I.887, A.888, D.889 Chain B: S.632, A.634, G.635 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.151, B:A.634 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.29: 13 residues within 4Å: Chain B: E.132, Y.151, K.152, N.411, S.413, N.419, F.437, I.887, A.888, D.889 Chain C: S.632, A.634, G.635 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.151, C:A.634 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.50: 13 residues within 4Å: Chain A: S.632, A.634, G.635 Chain C: E.132, Y.151, K.152, N.411, S.413, N.419, F.437, I.887, A.888, D.889 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.151, A:A.634

9 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.9: 5 residues within 4Å: Chain A: D.469, N.471, N.495, R.510, I.512 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain A: N.684, Q.695, Y.700 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 6 residues within 4Å: Chain A: W.1129, C.1180, V.1182, T.1183, F.1184, N.1186 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1182 NAG-NAG-BMA.30: 5 residues within 4Å: Chain B: D.469, N.471, N.495, R.510, I.512 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 3 residues within 4Å: Chain B: N.684, Q.695, Y.700 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 6 residues within 4Å: Chain B: W.1129, C.1180, V.1182, T.1183, F.1184, N.1186 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.1182 NAG-NAG-BMA.51: 5 residues within 4Å: Chain C: D.469, N.471, N.495, R.510, I.512 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.54: 3 residues within 4Å: Chain C: N.684, Q.695, Y.700 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.63: 6 residues within 4Å: Chain C: W.1129, C.1180, V.1182, T.1183, F.1184, N.1186 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.1182

6 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.11: 6 residues within 4Å: Chain A: V.459, S.605, L.607, N.651, S.653, T.654 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 6 residues within 4Å: Chain A: R.733, S.735, S.736, Y.1091, N.1096, L.1119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.736, A:S.736 NAG-NAG-BMA-MAN-MAN.32: 6 residues within 4Å: Chain B: V.459, S.605, L.607, N.651, S.653, T.654 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.40: 6 residues within 4Å: Chain B: R.733, S.735, S.736, Y.1091, N.1096, L.1119 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.736, B:S.736 NAG-NAG-BMA-MAN-MAN.53: 6 residues within 4Å: Chain C: V.459, S.605, L.607, N.651, S.653, T.654 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.61: 6 residues within 4Å: Chain C: R.733, S.735, S.736, Y.1091, N.1096, L.1119 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.736, C:S.736

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

NAG.64: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP NAG.65: 5 residues within 4Å: Chain A: T.31, H.32, F.34, V.170, N.172 Ligand excluded by PLIP NAG.66: 5 residues within 4Å: Chain A: S.22, I.24, N.178, C.192, C.195 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain A: N.495, N.497 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain A: N.610, N.611 Ligand excluded by PLIP NAG.69: 3 residues within 4Å: Chain A: S.628, S.629, N.630 Ligand excluded by PLIP NAG.70: 3 residues within 4Å: Chain A: N.1203, L.1206, Q.1207 Ligand excluded by PLIP NAG.71: 1 residues within 4Å: Chain B: N.140 Ligand excluded by PLIP NAG.72: 5 residues within 4Å: Chain B: T.31, H.32, F.34, V.170, N.172 Ligand excluded by PLIP NAG.73: 5 residues within 4Å: Chain B: S.22, I.24, N.178, C.192, C.195 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain B: N.495, N.497 Ligand excluded by PLIP NAG.75: 2 residues within 4Å: Chain B: N.610, N.611 Ligand excluded by PLIP NAG.76: 3 residues within 4Å: Chain B: S.628, S.629, N.630 Ligand excluded by PLIP NAG.77: 3 residues within 4Å: Chain B: N.1203, L.1206, Q.1207 Ligand excluded by PLIP NAG.78: 1 residues within 4Å: Chain C: N.140 Ligand excluded by PLIP NAG.79: 5 residues within 4Å: Chain C: T.31, H.32, F.34, V.170, N.172 Ligand excluded by PLIP NAG.80: 5 residues within 4Å: Chain C: S.22, I.24, N.178, C.192, C.195 Ligand excluded by PLIP NAG.81: 2 residues within 4Å: Chain C: N.495, N.497 Ligand excluded by PLIP NAG.82: 2 residues within 4Å: Chain C: N.610, N.611 Ligand excluded by PLIP NAG.83: 3 residues within 4Å: Chain C: S.628, S.629, N.630 Ligand excluded by PLIP NAG.84: 3 residues within 4Å: Chain C: N.1203, L.1206, Q.1207 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walls, A.C. et al., Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-09-14

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein