SMTL ID : 6wj2.1

CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 13 residues within 4Å: Chain F: K.38, S.39, G.40, S.41, G.42, K.43, T.44, S.45, H.150, K.151, D.153, L.154, I.187 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.40, F:S.41, F:G.42, F:K.43, F:T.44, F:T.44, F:S.45, F:I.187 Salt bridges: F:K.43, F:D.153

1 x L8S: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione(Non-covalent)

L8S.2: 17 residues within 4Å: Chain G: R.76, S.77, G.78, K.79, S.80, S.81, T.95, L.96, T.101, G.124, H.183, K.184, N.186, S.224, I.225, Y.226 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:R.76, G:S.77, G:G.78, G:K.79, G:K.79, G:T.95, G:T.101, G:G.124, G:K.184, G:N.186, G:N.186, G:I.225 Salt bridges: G:R.76, G:K.79

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain G: S.80, T.101 Ligands: L8S.2 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.80, G:T.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fromm, S.A. et al., Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-09-02

Peptides

Ragulator complex protein LAMTOR1: A
Ragulator complex protein LAMTOR2: B
Ragulator complex protein LAMTOR3: C
Ragulator complex protein LAMTOR4: D
Ragulator complex protein LAMTOR5: E
Ras-related GTP-binding protein A: F
Ras-related GTP-binding protein C: G
Sodium-coupled neutral amino acid transporter 9: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Ragulator complex protein LAMTOR1

Ragulator complex protein LAMTOR2

Ragulator complex protein LAMTOR3

Ragulator complex protein LAMTOR4

Ragulator complex protein LAMTOR5

Ras-related GTP-binding protein A

Ras-related GTP-binding protein C

Sodium-coupled neutral amino acid transporter 9

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