SMTL ID : 8jxd.1

Cryo-EM structure of rat megalin leg

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

homo-tetramer

Ligands

2 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: 9 residues within 4Å: Chain A: S.4054, P.4055, L.4057, N.4070, S.4072, S.4073, N.4124, F.4125, E.4126 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 9 residues within 4Å: Chain C: S.4054, P.4055, L.4057, N.4070, S.4072, S.4073, N.4124, F.4125, E.4126 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: L.4241, N.4329, S.4331, V.4332 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain C: L.4241, N.4329, S.4331, V.4332 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: K.3936, Q.3979, N.3980, R.3994 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.3980, A:N.3980, A:R.3994, A:R.3994 NAG.13: 4 residues within 4Å: Chain C: K.3936, Q.3979, N.3980, R.3994 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.3980, C:N.3980, C:R.3994, C:R.3994

12 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.3947, A:D.3950, A:V.3952, A:D.3960, A:E.3961 CA.5: 7 residues within 4Å: Chain A: D.4009, I.4010, E.4012, N.4025, S.4026, G.4028, S.4029 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.4009, A:I.4010, A:E.4012, A:E.4012, A:S.4026 CA.7: 6 residues within 4Å: Chain B: W.45, D.48, T.50, D.52, D.58, E.59 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.45, B:D.48, B:D.52, B:D.58, B:E.59 CA.8: 8 residues within 4Å: Chain B: W.85, V.86, C.87, D.88, D.90, D.92, D.98, E.99 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.85, B:D.88, B:D.92, B:D.98, B:E.99 CA.9: 5 residues within 4Å: Chain B: W.3778, D.3781, E.3783, D.3785, D.3791 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.3778, B:D.3781, B:E.3783, B:D.3785, B:D.3791 CA.10: 7 residues within 4Å: Chain B: L.3817, A.3818, D.3820, R.3822, D.3824, D.3830, E.3831 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.3817, B:D.3820, B:D.3824, B:D.3830, B:E.3831 CA.14: 6 residues within 4Å: Chain C: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Y.3947, C:D.3950, C:V.3952, C:D.3960, C:E.3961 CA.15: 7 residues within 4Å: Chain C: D.4009, I.4010, E.4012, N.4025, S.4026, G.4028, S.4029 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.4009, C:I.4010, C:E.4012, C:E.4012, C:S.4026 CA.17: 6 residues within 4Å: Chain D: W.45, D.48, T.50, D.52, D.58, E.59 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:W.45, D:D.48, D:D.52, D:D.58, D:E.59 CA.18: 8 residues within 4Å: Chain D: W.85, V.86, C.87, D.88, D.90, D.92, D.98, E.99 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:W.85, D:D.88, D:D.92, D:D.98, D:E.99 CA.19: 5 residues within 4Å: Chain D: W.3778, D.3781, E.3783, D.3785, D.3791 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:W.3778, D:D.3781, D:E.3783, D:D.3785, D:D.3791 CA.20: 7 residues within 4Å: Chain D: L.3817, A.3818, D.3820, R.3822, D.3824, D.3830, E.3831 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:L.3817, D:D.3820, D:D.3824, D:D.3830, D:E.3831

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.6: 4 residues within 4Å: Chain B: T.3799, C.3800, H.3801, P.3802 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.3802 Hydrogen bonds: B:T.3799, B:C.3800 A2G.16: 4 residues within 4Å: Chain D: T.3799, C.3800, H.3801, P.3802 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.3802 Hydrogen bonds: D:T.3799, D:C.3800

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, S. et al., Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-06-19

Peptides

LDL receptor related protein 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

LDL receptor related protein 2

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