SMTL ID : 7fd2.3 (2 other biounits)

Cryo-EM structure of an alphavirus, Getah virus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 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.1: 4 residues within 4Å: Chain A: H.116 Chain B: L.260, T.261, N.262 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 5 residues within 4Å: Chain D: H.116, E.209 Chain E: L.260, T.261, N.262 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.209, D:E.209 NAG-NAG-BMA-MAN.7: 5 residues within 4Å: Chain G: H.116, N.264 Chain H: L.260, T.261, N.262 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.10: 6 residues within 4Å: Chain J: H.116, E.209, N.264 Chain K: L.260, T.261, N.262 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.264

4 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 A: Q.30, R.134, S.136, N.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.134 NAG-NAG.5: 4 residues within 4Å: Chain D: Q.30, R.134, S.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain G: R.134, S.136, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain J: R.134, S.136, N.141 No protein-ligand interaction detected (PLIP)

4 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.3: 5 residues within 4Å: Chain A: C.63, F.95, E.99 Chain B: N.200, T.202 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain D: C.63, F.95 Chain E: N.200, T.202 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain G: C.63, F.95 Chain H: N.200, T.202, N.207 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain J: C.63, F.95, E.99 Chain K: N.200, T.202 No protein-ligand interaction detected (PLIP)

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

NAG.13: 6 residues within 4Å: Chain A: V.11, L.34, G.35, T.36, E.269, N.270 No protein-ligand interaction detected (PLIP) NAG.23: 6 residues within 4Å: Chain D: V.11, L.34, G.35, T.36, E.269, N.270 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.269 NAG.33: 6 residues within 4Å: Chain G: V.11, L.34, G.35, T.36, E.269, N.270 No protein-ligand interaction detected (PLIP) NAG.43: 6 residues within 4Å: Chain J: V.11, L.34, G.35, T.36, E.269, N.270 No protein-ligand interaction detected (PLIP)

4 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.14: 13 residues within 4Å: Chain A: N.396, Q.397, V.398, F.399 Chain B: I.355, Y.362, A.365, A.368, A.369, V.370, A.372, A.373 Ligands: CLR.17 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.355, B:V.370, B:A.373, A:F.399, A:F.399 Hydrogen bonds: A:Q.397, A:Q.397, A:F.399 PCW.24: 9 residues within 4Å: Chain D: N.396, Q.397, V.398, F.399, M.407, V.410 Chain E: A.372, A.373 Ligands: CLR.27 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:A.373, D:F.399, D:F.399 Hydrogen bonds: D:Q.397, D:Q.397, D:V.398, D:F.399 PCW.34: 11 residues within 4Å: Chain G: N.396, Q.397, V.398, F.399, M.407, V.410 Chain H: Y.362, V.370, A.373 Ligands: CLR.35, CLR.38 8 PLIP interactions: 2 interactions with chain H, 6 interactions with chain G Hydrophobic interactions: H:V.370, H:A.373, G:F.399, G:V.410 Hydrogen bonds: G:Q.397, G:Q.397, G:V.398, G:F.399 PCW.44: 12 residues within 4Å: Chain J: N.396, Q.397, V.398, F.399, M.407, V.410 Chain K: Y.362, A.365, A.369, A.373 Ligands: CLR.47, CLR.48 8 PLIP interactions: 2 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:A.365, K:A.373, J:V.410, J:V.410 Hydrogen bonds: J:Q.397, J:Q.397, J:V.398, J:F.399

8 x STE: STEARIC ACID(Non-covalent)

STE.15: 4 residues within 4Å: Chain A: L.430, V.431, V.434, R.438 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.430, A:V.431 Salt bridges: A:R.438 STE.21: 3 residues within 4Å: Chain B: R.392, P.418 Ligands: PLM.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.418 STE.25: 4 residues within 4Å: Chain D: L.430, V.431, V.434, R.438 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.430, D:V.431 Salt bridges: D:R.438 STE.31: 4 residues within 4Å: Chain D: L.420 Chain E: R.392, P.418 Ligands: PLM.32 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.418 STE.37: 5 residues within 4Å: Chain G: L.430, V.431, V.434, R.438 Chain H: C.395 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:L.430, G:V.431 Salt bridges: G:R.438 STE.41: 3 residues within 4Å: Chain H: S.384, R.392 Ligands: PLM.42 No protein-ligand interaction detected (PLIP) STE.45: 7 residues within 4Å: Chain J: L.430, V.431, V.434, R.438 Chain K: C.395, L.411 Ligands: PLM.50 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:L.430, J:V.431, K:L.411 Salt bridges: J:R.438 STE.51: 5 residues within 4Å: Chain J: L.420 Chain K: S.384, R.392, P.418 Ligands: PLM.52 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:P.418

12 x PLM: PALMITIC ACID(Non-covalent)

PLM.16: 1 residues within 4Å: Chain A: M.436 No protein-ligand interaction detected (PLIP) PLM.20: 9 residues within 4Å: Chain A: G.416, G.419, L.420, A.423, V.427 Chain B: F.388, R.392, L.414, C.415 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.414, A:A.423, A:V.427 PLM.22: 5 residues within 4Å: Chain B: F.388, L.414, C.415, C.416 Ligands: STE.21 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.388 PLM.26: 1 residues within 4Å: Chain D: M.436 No protein-ligand interaction detected (PLIP) PLM.30: 6 residues within 4Å: Chain D: L.420, V.427 Chain E: F.388, R.392, L.414, C.415 No protein-ligand interaction detected (PLIP) PLM.32: 5 residues within 4Å: Chain E: F.388, L.414, C.415, C.416 Ligands: STE.31 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.388 PLM.36: 1 residues within 4Å: Chain G: M.436 No protein-ligand interaction detected (PLIP) PLM.40: 9 residues within 4Å: Chain G: L.420, A.423, V.427 Chain H: F.388, A.391, R.392, C.395, L.414, C.415 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:F.388, G:A.423 PLM.42: 5 residues within 4Å: Chain H: F.388, L.414, C.415, C.416 Ligands: STE.41 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.388 PLM.46: 1 residues within 4Å: Chain J: M.436 No protein-ligand interaction detected (PLIP) PLM.50: 10 residues within 4Å: Chain J: G.419, L.420, A.423, V.427, V.431 Chain K: F.388, R.392, L.414, C.415 Ligands: STE.45 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:A.423, J:V.427 PLM.52: 5 residues within 4Å: Chain K: F.388, L.414, C.415, C.416 Ligands: STE.51 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:F.388

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 15 residues within 4Å: Chain A: F.399, P.400, A.406, M.407, W.409, V.410 Chain B: P.351, I.354, I.355, Y.358, Y.362, A.365, T.366, A.369 Ligands: PCW.14 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.399, A:A.406, A:W.409, A:V.410, B:I.354, B:Y.358, B:Y.362, B:A.365, B:A.369 CLR.18: 4 residues within 4Å: Chain B: I.355, L.356, G.374 Ligands: CLR.19 No protein-ligand interaction detected (PLIP) CLR.19: 8 residues within 4Å: Chain B: I.355, Y.359, I.367, V.370, S.371, G.374, L.375 Ligands: CLR.18 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.355, B:Y.359, B:Y.359, B:I.367, B:V.370, B:L.375 CLR.27: 12 residues within 4Å: Chain D: A.406, M.407 Chain E: P.351, I.354, I.355, Y.358, Y.362, A.365, T.366, A.369, V.370 Ligands: PCW.24 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.354, E:I.354, E:I.355, E:Y.358, E:Y.362, E:A.365, E:A.369, E:V.370 CLR.28: 5 residues within 4Å: Chain E: H.352, I.355, L.356, G.374 Ligands: CLR.29 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:H.352 CLR.29: 9 residues within 4Å: Chain E: I.355, L.356, Y.359, I.367, V.370, S.371, G.374, L.375 Ligands: CLR.28 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:I.355, E:L.356, E:Y.359, E:Y.359, E:I.367, E:V.370 CLR.35: 14 residues within 4Å: Chain G: V.398, P.400, A.406, M.407, W.409, V.410 Chain H: P.351, I.354, I.355, Y.358, Y.362, A.365, T.366 Ligands: PCW.34 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain H Hydrophobic interactions: G:V.398, G:P.400, G:A.406, G:W.409, G:V.410, H:I.354, H:Y.358, H:Y.358, H:Y.362, H:A.365 CLR.38: 5 residues within 4Å: Chain H: I.355, L.356, G.374 Ligands: PCW.34, CLR.39 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:I.355, H:L.356 CLR.39: 6 residues within 4Å: Chain H: L.356, Y.359, V.370, S.371, G.374 Ligands: CLR.38 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.359, H:Y.359 CLR.47: 15 residues within 4Å: Chain J: V.398, P.400, A.406, M.407, W.409 Chain K: P.351, I.354, I.355, Y.358, Y.362, A.365, T.366, A.369, V.370 Ligands: PCW.44 10 PLIP interactions: 3 interactions with chain J, 7 interactions with chain K Hydrophobic interactions: J:V.398, J:A.406, J:W.409, K:I.354, K:I.354, K:Y.358, K:Y.362, K:A.365, K:A.369, K:V.370 CLR.48: 8 residues within 4Å: Chain K: H.352, I.355, L.356, V.370, G.374, V.377 Ligands: PCW.44, CLR.49 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:H.352, K:I.355, K:L.356, K:V.377 CLR.49: 6 residues within 4Å: Chain K: L.356, Y.359, I.367, V.370, S.371 Ligands: CLR.48 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:L.356, K:Y.359, K:Y.359, K:V.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, A. et al., Structure of infective Getah virus at 2.8 angstrom resolution determined by cryo-electron microscopy. Cell Discov (2022)

Release Date

2022-08-10

Peptides

Envelope glycoprotein 1: ADGJ
Envelope glycoprotein 2: BEHK
capsid protein: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

G
I

J
M

B
B

E
F

H
J

K
N

C
C

F
G

I
K

L
O

Envelope glycoprotein 1

Envelope glycoprotein 2

capsid protein

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