SMTL ID : 7ndg.1

Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: F.83, D.86, T.94, S.253 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.83, A:D.86, A:T.94, A:T.94, A:S.253 CA.6: 4 residues within 4Å: Chain F: F.83, D.86, T.94, S.253 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:F.83, F:D.86, F:T.94, F:T.94, F:S.253 CA.11: 4 residues within 4Å: Chain I: F.83, D.86, T.94, S.253 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:F.83, I:D.86, I:T.94, I:T.94, I:S.253

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

NAG.2: 4 residues within 4Å: Chain A: P.75, K.76, N.92, T.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.92 NAG.3: 3 residues within 4Å: Chain A: N.107, Y.138, A.226 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.138, A:A.226 NAG.4: 4 residues within 4Å: Chain A: P.50, N.71, S.73, D.74 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.74 NAG.5: 4 residues within 4Å: Chain B: Y.143, N.160, A.161, N.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.162 NAG.7: 4 residues within 4Å: Chain F: P.75, K.76, N.92, T.94 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.92 NAG.8: 3 residues within 4Å: Chain F: N.107, Y.138, A.226 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.138, F:A.226 NAG.9: 4 residues within 4Å: Chain F: P.50, N.71, S.73, D.74 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:D.74 NAG.10: 4 residues within 4Å: Chain G: Y.143, N.160, A.161, N.162 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.162 NAG.12: 4 residues within 4Å: Chain I: P.75, K.76, N.92, T.94 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.92 NAG.13: 3 residues within 4Å: Chain I: N.107, Y.138, A.226 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.138, I:A.226 NAG.14: 4 residues within 4Å: Chain I: P.50, N.71, S.73, D.74 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:D.74 NAG.15: 4 residues within 4Å: Chain J: Y.143, N.160, A.161, N.162 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, R.A. et al., Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling. Cell (2021)

Release Date

2021-03-31

Peptides

Netrin-1: AFI
Neogenin: BGJ
Repulsive Guidance Molecule B (C-terminal region): CEK
RGM domain family member B: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
G

I
D

B
B

G
H

J
E

C
F

E
C

K
I

D
N

H
M

L
O

Netrin-1

Neogenin

Repulsive Guidance Molecule B (C-terminal region)

RGM domain family member B

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