SMTL ID : 6q2r.1

Cryo-EM structure of RET/GFRa2/NRTN extracellular complex in the tetrameric form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

16 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain D: E.150, N.151, D.202, E.204, D.239 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.150, D:D.202, D:D.239 CA.2: 6 residues within 4Å: Chain D: E.204, D.236, E.237, D.239, A.273, 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:S.240, D:D.272, 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 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.150, F:D.202, F:D.239 CA.12: 6 residues within 4Å: Chain F: E.204, D.236, E.237, D.239, A.273, 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:S.240, F:D.272, 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 CA.21: 5 residues within 4Å: Chain J: E.150, N.151, D.202, E.204, D.239 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.150, J:D.202, J:D.239 CA.22: 6 residues within 4Å: Chain J: E.204, D.236, E.237, D.239, A.273, D.274 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.204, J:D.236, J:E.237, J:D.239, J:D.274 CA.23: 6 residues within 4Å: Chain J: D.238, S.240, D.272, D.274, Y.286, D.350 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.238, J:S.240, J:D.272, J:D.350, J:D.350 CA.24: 6 residues within 4Å: Chain J: T.536, C.537, D.539, H.541, E.546, D.556 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:T.536, J:D.539, J:H.541, J:E.546, J:D.556 CA.31: 5 residues within 4Å: Chain L: E.150, N.151, D.202, E.204, D.239 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.150, L:D.202, L:D.239 CA.32: 6 residues within 4Å: Chain L: E.204, D.236, E.237, D.239, A.273, D.274 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.204, L:D.236, L:E.237, L:D.239, L:D.274 CA.33: 6 residues within 4Å: Chain L: D.238, S.240, D.272, D.274, Y.286, D.350 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:D.238, L:S.240, L:D.272, L:D.350, L:D.350 CA.34: 6 residues within 4Å: Chain L: T.536, C.537, D.539, H.541, E.546, D.556 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:T.536, L:D.539, L:H.541, L:E.546, L:D.556

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

NAG.5: 3 residues within 4Å: Chain D: N.349, S.351, V.360 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain D: T.250, N.366 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain D: F.438, N.440 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain D: N.339, P.371 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain C: R.303 Chain D: W.306, N.308 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain D: N.333, G.407, N.409 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain F: N.349, S.351, V.360 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain F: T.250, N.366 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain F: F.438, N.440 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain F: N.339, P.371 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain E: R.303 Chain F: W.306, N.308 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain F: N.333, G.407, N.409 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain J: N.349, S.351, V.360 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain J: T.250, N.366 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain J: F.438, N.440 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain J: N.339, P.371 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain I: R.303 Chain J: W.306, N.308 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain J: N.333, G.407, N.409 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain L: N.349, S.351, V.360 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain L: T.250, N.366 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain L: F.438, N.440 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain L: N.339, P.371 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: R.303 Chain L: W.306, N.308 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain L: N.333, G.407, N.409 Ligand excluded by PLIP

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: ABGH
GDNF family receptor alpha-2: CEIK
Proto-oncogene tyrosine-protein kinase receptor Ret: DFJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

G
U

H
V

C
C

E
D

I
W

K
X

D
E

F
F

J
Y

L
Z

Neurturin

GDNF family receptor alpha-2

Proto-oncogene tyrosine-protein kinase receptor Ret

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