SMTL ID : 6q2o.1

Cryo-EM structure of RET/GFRa2/NRTN extracellular complex. The 3D refinement was applied with C2 symmetry.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain D: E.150, N.151, D.202, E.204, D.239 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.150, D:E.150, D:D.202, D:E.204, D:D.239 CA.2: 5 residues within 4Å: Chain D: E.204, D.236, E.237, D.239, D.274 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.204, D:D.236, D:E.237, D:D.239, D:D.274 CA.3: 6 residues within 4Å: Chain D: D.238, S.240, D.272, D.274, Y.286, D.350 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.238, D:D.272, D:Y.286, D:D.350, D:D.350 CA.4: 6 residues within 4Å: Chain D: T.536, C.537, D.539, H.541, E.546, D.556 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:T.536, D:D.539, D:H.541, D:E.546, D:D.556 CA.11: 5 residues within 4Å: Chain F: E.150, N.151, D.202, E.204, D.239 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.150, F:E.150, F:D.202, F:E.204, F:D.239 CA.12: 5 residues within 4Å: Chain F: E.204, D.236, E.237, D.239, D.274 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.204, F:D.236, F:E.237, F:D.239, F:D.274 CA.13: 6 residues within 4Å: Chain F: D.238, S.240, D.272, D.274, Y.286, D.350 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.238, F:D.272, F:Y.286, F:D.350, F:D.350 CA.14: 6 residues within 4Å: Chain F: T.536, C.537, D.539, H.541, E.546, D.556 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:T.536, F:D.539, F:H.541, F:E.546, F:D.556

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

NAG.5: 2 residues within 4Å: Chain D: N.349, V.360 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.360 Hydrogen bonds: D:N.349 NAG.6: 3 residues within 4Å: Chain D: T.250, Q.343, N.366 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.250 NAG.7: 3 residues within 4Å: Chain D: V.426, F.438, N.440 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.438 Hydrogen bonds: D:N.440 NAG.8: 2 residues within 4Å: Chain D: N.339, P.371 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.371 NAG.9: 2 residues within 4Å: Chain C: R.303 Chain D: N.308 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.303, D:N.308 NAG.10: 4 residues within 4Å: Chain D: N.333, S.406, G.407, N.409 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.333 NAG.15: 2 residues within 4Å: Chain F: N.349, V.360 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.360 Hydrogen bonds: F:N.349 NAG.16: 3 residues within 4Å: Chain F: T.250, Q.343, N.366 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.250 NAG.17: 3 residues within 4Å: Chain F: V.426, F.438, N.440 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.438 Hydrogen bonds: F:N.440 NAG.18: 2 residues within 4Å: Chain F: N.339, P.371 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.371 NAG.19: 2 residues within 4Å: Chain E: R.303 Chain F: N.308 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.303, F:N.308 NAG.20: 4 residues within 4Å: Chain F: N.333, S.406, G.407, N.409 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. Elife (2019)

Release Date

2019-10-02

Peptides

Neurturin: AB
GDNF family receptor alpha-2: CE
Proto-oncogene tyrosine-protein kinase receptor Ret: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
D

D
E

F
F

Neurturin

GDNF family receptor alpha-2

Proto-oncogene tyrosine-protein kinase receptor Ret

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