SMTL ID : 7asd.1 (1 other biounit)

Structure of native royal jelly filaments

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.84, V.143, N.144, Q.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 NAG-NAG.3: 4 residues within 4Å: Chain C: N.84, V.143, N.144, Q.147 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.84 NAG-NAG.5: 4 residues within 4Å: Chain E: N.84, V.143, N.144, Q.147 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.84 NAG-NAG.7: 4 residues within 4Å: Chain G: N.84, V.143, N.144, Q.147 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.84

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.2: 7 residues within 4Å: Chain A: N.177, T.180, E.211, T.227, S.228, N.229, D.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.232, A:D.232 NAG-NAG-BMA.4: 7 residues within 4Å: Chain C: N.177, T.180, E.211, T.227, S.228, N.229, D.232 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.227, C:D.232 NAG-NAG-BMA.6: 7 residues within 4Å: Chain E: N.177, T.180, E.211, T.227, S.228, N.229, D.232 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.227, E:D.232 NAG-NAG-BMA.8: 7 residues within 4Å: Chain G: N.177, T.180, E.211, T.227, S.228, N.229, D.232 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.232, G:D.232

8 x 94R: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol(Non-covalent)

94R.9: 11 residues within 4Å: Chain A: P.364, V.366, I.373, R.375, I.430 Chain B: I.42 Chain C: F.369, F.426 Ligands: 94R.12, 94R.13, 94R.16 8 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:F.369, C:F.426, B:I.42, A:V.366, A:I.373, A:I.430 Hydrogen bonds: A:V.366, A:R.375 94R.12: 10 residues within 4Å: Chain B: V.55 Chain D: L.45, L.60, L.64, I.67, L.71, F.77 Ligands: 94R.9, 94R.13, 94R.16 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.45, D:L.60, D:L.64, D:I.67, D:F.77 94R.13: 11 residues within 4Å: Chain A: F.369, F.426 Chain C: P.364, V.366, I.373, R.375, I.430 Chain D: I.42 Ligands: 94R.9, 94R.12, 94R.16 8 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:F.369, A:F.426, C:V.366, C:I.373, C:I.430, D:I.42 Hydrogen bonds: C:V.366, C:R.375 94R.16: 11 residues within 4Å: Chain B: L.45, L.60, L.64, I.67, L.71, F.77 Chain D: I.49, V.55 Ligands: 94R.9, 94R.12, 94R.13 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.45, B:L.60, B:L.64, B:I.67, B:F.77, D:I.49 94R.17: 11 residues within 4Å: Chain E: P.364, V.366, I.373, R.375, I.430 Chain F: I.42 Chain G: F.369, F.426 Ligands: 94R.20, 94R.21, 94R.24 9 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: E:V.366, E:I.373, E:I.430, F:I.42, G:F.369, G:F.426, G:F.426 Hydrogen bonds: E:V.366, E:R.375 94R.20: 10 residues within 4Å: Chain F: V.55 Chain H: L.45, L.60, L.64, I.67, L.71, F.77 Ligands: 94R.17, 94R.21, 94R.24 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:L.45, H:L.60, H:L.64, H:I.67, H:F.77 94R.21: 11 residues within 4Å: Chain E: F.369, F.426 Chain G: P.364, V.366, I.373, R.375, I.430 Chain H: I.42 Ligands: 94R.17, 94R.20, 94R.24 9 PLIP interactions: 3 interactions with chain E, 5 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: E:F.369, E:F.426, E:F.426, G:V.366, G:I.373, G:I.430, H:I.42 Hydrogen bonds: G:V.366, G:R.375 94R.24: 10 residues within 4Å: Chain F: L.45, L.60, L.64, I.67, L.71, F.77 Chain H: V.55 Ligands: 94R.17, 94R.20, 94R.21 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.45, F:L.60, F:L.64, F:I.67, F:F.77

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

NAG.10: 1 residues within 4Å: Chain A: N.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 NAG.14: 1 residues within 4Å: Chain C: N.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.28 NAG.18: 1 residues within 4Å: Chain E: N.28 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.28 NAG.22: 1 residues within 4Å: Chain G: N.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.28

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 5 residues within 4Å: Chain A: R.23, R.342, R.415 Chain C: R.23 Ligands: SO4.15 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.23, A:R.415 Salt bridges: A:R.342, A:R.415 SO4.15: 5 residues within 4Å: Chain A: R.23 Chain C: R.23, R.342, R.415 Ligands: SO4.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.415 Salt bridges: C:R.342, C:R.415, A:R.23 SO4.19: 5 residues within 4Å: Chain E: R.23, R.342, R.415 Chain G: R.23 Ligands: SO4.23 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain E Hydrogen bonds: G:R.23, E:R.415 Salt bridges: E:R.342, E:R.415 SO4.23: 5 residues within 4Å: Chain E: R.23 Chain G: R.23, R.342, R.415 Ligands: SO4.19 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:R.415, E:R.23 Salt bridges: G:R.342, G:R.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mattei, S. et al., Structure of native glycolipoprotein filaments in honeybee royal jelly. Nat Commun (2020)

Release Date

2020-12-30

Peptides

Major royal jelly protein 1: ACEG
Apisimin: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

C
BA

E
CA

G
DA

B
AB

D
BB

F
CB

H
DB

Major royal jelly protein 1

Apisimin

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