SMTL ID : 9lwf.1

Cryo-EM structure of dual sensor bound GATOR2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.41 Å

Oligo State

hetero-4-2-2-6-2-2-2-mer

Ligands

32 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.737, C.740, C.775, C.778 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.737, A:C.740, A:C.775, A:C.778 ZN.2: 4 residues within 4Å: Chain A: C.785, C.788, H.835, H.838 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.785, A:C.788, A:H.835, A:H.838 ZN.3: 4 residues within 4Å: Chain A: C.827, C.830, C.856, C.858 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.827, A:C.830, A:C.856, A:C.858 ZN.4: 4 residues within 4Å: Chain A: C.830, H.832, C.849, C.854 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.830, A:H.832, A:C.849, A:C.854 ZN.5: 3 residues within 4Å: Chain B: C.737, F.739, C.740 No protein-ligand interaction detected (PLIP) ZN.6: 4 residues within 4Å: Chain B: C.785, C.788, H.835, H.838 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.785, B:C.788, B:H.835, B:H.838 ZN.7: 4 residues within 4Å: Chain B: C.827, C.830, C.856, C.858 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.827, B:C.856, B:C.858 ZN.8: 4 residues within 4Å: Chain B: C.830, H.832, C.849, C.854 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.832, B:C.849 ZN.9: 3 residues within 4Å: Chain C: H.721, R.738 Chain J: A.731 No protein-ligand interaction detected (PLIP) ZN.10: 3 residues within 4Å: Chain C: V.745, H.768 Chain J: H.711 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.768 ZN.11: 3 residues within 4Å: Chain C: H.785, L.786, C.787 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.787 ZN.12: 4 residues within 4Å: Chain C: H.778, C.779, G.784, H.785 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.785 ZN.13: 4 residues within 4Å: Chain D: C.902, C.905, C.914, C.917 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.902, D:C.905, D:C.914, D:C.917 ZN.14: 4 residues within 4Å: Chain D: C.924, C.927, H.946, H.949 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.924, D:C.927, D:H.946, D:H.949 ZN.15: 4 residues within 4Å: Chain D: C.938, C.941, C.966, C.968 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.938, D:C.941, D:C.966, D:C.968 ZN.16: 5 residues within 4Å: Chain D: C.941, H.943, C.960, T.962, C.964 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.943, D:C.960, D:C.964 ZN.17: 4 residues within 4Å: Chain I: C.719, C.722, C.733, C.736 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.719, I:C.722, I:C.733, I:C.736 ZN.18: 4 residues within 4Å: Chain I: C.743, C.746, H.765, H.768 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.743, I:C.746, I:H.765, I:H.768 ZN.19: 4 residues within 4Å: Chain I: C.757, C.760, H.785, C.787 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.757, I:C.760, I:H.785, I:C.787 ZN.20: 4 residues within 4Å: Chain I: C.760, H.762, C.779, C.783 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.760, I:H.762, I:C.779, I:C.783 ZN.21: 4 residues within 4Å: Chain J: C.737, C.740, C.775, C.778 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.737, J:C.740, J:C.775, J:C.778 ZN.22: 4 residues within 4Å: Chain J: C.785, C.788, H.835, H.838 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.785, J:C.788, J:H.835, J:H.838 ZN.23: 5 residues within 4Å: Chain J: C.827, N.829, C.830, C.856, C.858 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.827, J:C.830, J:C.858 ZN.24: 4 residues within 4Å: Chain J: C.830, H.832, C.849, C.854 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.830, J:H.832, J:C.849, J:C.854 ZN.25: 4 residues within 4Å: Chain K: C.737, C.740, C.775, C.778 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:C.740 ZN.26: 4 residues within 4Å: Chain K: C.785, C.788, H.835, H.838 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:H.838, K:H.838 ZN.27: 4 residues within 4Å: Chain K: C.827, C.830, C.856, C.858 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.827, K:C.830, K:C.856 ZN.28: 5 residues within 4Å: Chain K: C.830, H.832, C.849, V.851, C.854 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:H.832, K:C.849, K:C.854 ZN.29: 4 residues within 4Å: Chain L: C.902, C.905, C.914, C.917 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.902, L:C.905, L:C.914, L:C.917 ZN.30: 4 residues within 4Å: Chain L: C.924, C.927, H.946, H.949 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.924, L:C.927, L:H.946, L:H.949 ZN.31: 5 residues within 4Å: Chain L: C.938, T.940, C.941, C.966, C.968 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.938, L:C.941, L:C.966, L:C.968 ZN.32: 5 residues within 4Å: Chain L: C.941, H.943, C.960, C.964, C.966 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.941, L:H.943, L:C.960, L:C.964

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, M.Y. et al., Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex. Cell Rep (2025)

Release Date

2025-08-13

Peptides

GATOR2 complex protein MIOS: ABJK
GATOR2 complex protein WDR24: CI
GATOR2 complex protein WDR59: DL
Isoform B of Nucleoporin SEH1: EFGMNO
Isoform 3 of Protein SEC13 homolog: HP
Cytosolic arginine sensor for mTORC1 subunit 1: QR
Sestrin-2: ST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

J
K

K
L

C
C

I
I

D
D

L
N

E
E

F
F

G
G

M
O

N
P

O
Q

H
H

P
R

Q
U

R
V

S
X

T
Y

GATOR2 complex protein MIOS

GATOR2 complex protein WDR24

GATOR2 complex protein WDR59

Isoform B of Nucleoporin SEH1

Isoform 3 of Protein SEC13 homolog

Cytosolic arginine sensor for mTORC1 subunit 1

Sestrin-2

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