SMTL ID : 7aml.1

RET/GDNF/GFRa1 extracellular complex Cryo-EM structure

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.143, N.144, D.195, R.196, E.197, D.232 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.143, A:E.143, A:D.195, A:E.197, A:D.232 CA.2: 7 residues within 4Å: Chain A: E.143, E.197, D.229, E.230, D.231, D.232, D.266 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.143, A:E.197, A:D.229, A:D.229, A:D.266 CA.3: 8 residues within 4Å: Chain A: D.231, N.233, S.234, D.264, D.266, N.278, D.342, F.345 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.231, A:N.233, A:D.264, A:D.266, A:D.342 CA.4: 8 residues within 4Å: Chain A: T.538, C.539, D.541, Y.543, C.544, D.545, E.548, D.558 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.538, A:Y.543, A:D.558 CA.12: 6 residues within 4Å: Chain B: E.143, N.144, D.195, R.196, E.197, D.232 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.143, B:E.143, B:D.195, B:E.197, B:D.232 CA.13: 7 residues within 4Å: Chain B: E.143, E.197, D.229, E.230, D.231, D.232, D.266 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.143, B:E.197, B:D.229, B:D.229, B:D.266 CA.14: 8 residues within 4Å: Chain B: D.231, N.233, S.234, D.264, D.266, N.278, D.342, F.345 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.231, B:N.233, B:D.264, B:D.266, B:D.342 CA.15: 9 residues within 4Å: Chain B: T.538, C.539, D.541, G.542, Y.543, C.544, D.545, E.548, D.558 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.538, B:E.548

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

NAG.5: 3 residues within 4Å: Chain A: Y.236, V.237, N.238 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: L.284, M.285, T.286, N.287 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: E.253, Q.324, N.325, G.399, D.401 Ligand excluded by PLIP NAG.8: 7 residues within 4Å: Chain A: L.339, N.341, D.342, T.343, F.345, P.346, T.351 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: D.244, L.335, N.357, T.359 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: W.422, S.425, N.440, D.441 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: R.489, F.490, L.508, N.551, I.552, S.553 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: Y.236, V.237, N.238 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: L.284, M.285, T.286, N.287 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain B: E.253, Q.324, N.325, G.399, D.401 Ligand excluded by PLIP NAG.19: 7 residues within 4Å: Chain B: L.339, N.341, D.342, T.343, F.345, P.346, T.351 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: D.244, N.357, T.359 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: W.422, S.425, N.440, D.441 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain B: R.489, F.490, L.508, N.551, I.552, S.553 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: L.15, N.16, D.19 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain F: L.15, N.16, D.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, S.E. et al., A two-site flexible clamp mechanism for RET-GDNF-GFR alpha 1 assembly reveals both conformational adaptation and strict geometric spacing. Structure (2021)

Release Date

2021-01-13

Peptides

Proto-oncogene tyrosine-protein kinase receptor Ret: AB
GDNF family receptor alpha: CE
Glial cell line-derived neurotrophic factor: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

E
E

D
C

F
F

Proto-oncogene tyrosine-protein kinase receptor Ret

GDNF family receptor alpha

Glial cell line-derived neurotrophic factor