SMTL ID : 8jxa.1

cryo-EM structure of rat megalin bodyB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

1 x UNK- UNK- ASN- UNK- UNK: unclear peptide(Non-covalent)

UNK-UNK-ASN-UNK-UNK.1: 6 residues within 4Å: Chain A: R.3326, W.3342, N.3370, H.3411, K.3452, R.3738 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.3326, A:R.3326, A:N.3370, A:N.3370, A:K.3452, A:R.3738

2 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: 2 residues within 4Å: Chain A: H.3126, N.3127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: Y.3202, N.3213, I.3224, L.3258 No protein-ligand interaction detected (PLIP)

3 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.4: 3 residues within 4Å: Chain A: E.3240, N.3259, T.3261 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.3240 NAG-NAG-BMA-MAN-MAN.7: 4 residues within 4Å: Chain A: D.3564, N.3566, A.3581, A.3847 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain A: P.3551, H.3552, R.3563, F.3838, N.3840, T.3842, P.3845, A.3846 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.3552 Hydrogen bonds: A:A.3846, A:R.3563

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.5: 1 residues within 4Å: Chain A: N.3317 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: H.3336, R.3350, N.3357, S.3359, E.3397, A.3486 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: P.4055, N.4070, F.4125, E.4126, H.4387 No protein-ligand interaction detected (PLIP)

1 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.10: 2 residues within 4Å: Chain B: N.4329, S.4331 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain A: V.3445, L.3446, N.3448 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.3448 NAG.12: 2 residues within 4Å: Chain A: H.3068, N.3682 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.3682

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

A2G.13: 1 residues within 4Å: Chain A: T.1225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1225 A2G.14: 2 residues within 4Å: Chain A: T.1271, C.1272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.1272 A2G.15: 2 residues within 4Å: Chain A: T.3636, C.3637 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.3636 A2G.16: 2 residues within 4Å: Chain A: T.3799, C.3800 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.3799 A2G.17: 3 residues within 4Å: Chain A: T.3836, F.3838, P.3839 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.3836

20 x CA: CALCIUM ION(Non-covalent)

CA.18: 6 residues within 4Å: Chain A: W.1249, D.1252, H.1254, D.1256, D.1262, E.1263 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.1249, A:D.1252, A:H.1254, A:D.1256, A:E.1263 CA.19: 8 residues within 4Å: Chain A: W.2925, V.2926, C.2927, D.2928, D.2930, D.2932, D.2938, E.2939 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.2925, A:D.2928, A:D.2932, A:D.2938, A:E.2939 CA.20: 8 residues within 4Å: Chain A: W.2972, V.2973, C.2974, D.2975, D.2977, D.2979, D.2985, E.2986 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:W.2972, A:D.2975, A:E.2986 CA.21: 6 residues within 4Å: Chain A: F.3012, D.3015, R.3017, D.3019, D.3025, E.3026 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.3012, A:D.3015, A:R.3017, A:D.3019, A:D.3025 CA.22: 6 residues within 4Å: Chain A: F.3051, D.3054, D.3056, D.3058, D.3064, E.3065 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.3051, A:D.3054, A:D.3058, A:D.3064, A:E.3065 CA.23: 5 residues within 4Å: Chain A: R.3094, N.3097, V.3099, D.3107, E.3108 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.3094, A:V.3099, A:E.3108 CA.24: 7 residues within 4Å: Chain A: D.3154, I.3155, E.3157, N.3171, V.3172, G.3174, S.3175 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3154, A:I.3155, A:E.3157, A:E.3157, A:V.3172 CA.25: 3 residues within 4Å: Chain A: A.3291, D.3294, E.3323 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.3291, A:D.3294, A:E.3323 CA.26: 2 residues within 4Å: Chain A: V.3344, E.3367 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.3344, A:E.3367 CA.27: 3 residues within 4Å: Chain A: A.3386, H.3387, P.3410 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.3410 CA.28: 6 residues within 4Å: Chain A: W.3532, D.3535, Q.3537, D.3539, D.3545, E.3546 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3532, A:D.3535, A:Q.3537, A:D.3539, A:E.3546 CA.29: 6 residues within 4Å: Chain A: A.3572, N.3575, R.3577, D.3579, D.3585, E.3586 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.3572, A:R.3577, A:D.3579, A:D.3585, A:E.3586 CA.30: 7 residues within 4Å: Chain A: W.3613, C.3615, D.3616, V.3618, D.3620, D.3626, E.3627 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3613, A:D.3616, A:D.3620, A:D.3626, A:E.3627 CA.31: 6 residues within 4Å: Chain A: W.3654, D.3657, D.3659, D.3661, D.3667, E.3668 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3654, A:D.3659, A:D.3661, A:D.3667, A:E.3668 CA.32: 6 residues within 4Å: Chain A: A.3699, N.3702, F.3704, D.3706, D.3712, E.3713 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.3699, A:F.3704, A:D.3706, A:D.3712, A:E.3713 CA.33: 6 residues within 4Å: Chain A: W.3739, D.3742, T.3744, D.3746, D.3752, E.3753 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.3742, A:T.3744, A:D.3746, A:D.3752, A:E.3753 CA.34: 7 residues within 4Å: Chain A: W.3778, C.3780, D.3781, E.3783, D.3785, D.3791, E.3792 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3778, A:E.3783, A:D.3785, A:D.3791, A:E.3792 CA.35: 7 residues within 4Å: Chain A: L.3817, C.3819, D.3820, R.3822, D.3824, D.3830, E.3831 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.3817, A:D.3820, A:R.3822, A:D.3824, A:D.3830 CA.36: 7 residues within 4Å: Chain A: W.3861, C.3863, D.3864, E.3866, D.3868, D.3874, E.3875 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.3861, A:D.3864, A:D.3868, A:D.3874, A:E.3875 CA.37: 7 residues within 4Å: Chain A: Q.3903, N.3906, V.3908, D.3909, D.3910, D.3916, E.3917 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Q.3903, A:V.3908, A:D.3910, A:D.3916, A:E.3917

Links

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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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LDL receptor related protein 2

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