SMTL ID : 9lvj.1

Cryo-EM structure of Sestrin2 bound human GATOR2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.82 Å

Oligo State

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

Ligands

32 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: C.737, C.740, G.741 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.737, A:C.740 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.830, A:H.832, A:H.832, A:C.849, A:C.854 ZN.5: 3 residues within 4Å: Chain B: C.740, G.741, K.742 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.741 ZN.6: 3 residues within 4Å: Chain B: C.785, C.788, H.835 No protein-ligand interaction detected (PLIP) ZN.7: 6 residues within 4Å: Chain B: C.827, H.828, N.829, C.830, R.831, C.858 No protein-ligand interaction detected (PLIP) ZN.8: 6 residues within 4Å: Chain B: C.830, H.832, C.849, V.851, C.854, C.856 No protein-ligand interaction detected (PLIP) ZN.9: 5 residues within 4Å: Chain C: C.719, H.721, C.722, C.733, C.736 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.719, C:C.722, C:C.733, C:C.736 ZN.10: 4 residues within 4Å: Chain C: C.743, C.746, H.765, H.768 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.743, C:C.746, C:H.765, C:H.768 ZN.11: 4 residues within 4Å: Chain C: C.757, C.760, H.785, C.787 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.757, C:C.760, C:H.785, C:C.787 ZN.12: 4 residues within 4Å: Chain C: C.760, H.762, C.779, C.783 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.760, C:H.762, C:C.779, C:C.783 ZN.13: 4 residues within 4Å: Chain D: C.902, C.905, C.914, C.917 3 PLIP interactions: 3 interactions with chain D Metal complexes: 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 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.924, D:C.927, D:H.949 ZN.15: 5 residues within 4Å: Chain D: C.938, T.940, 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: 4 residues within 4Å: Chain D: C.941, H.943, C.960, C.964 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.941, D:H.943, D:C.960, D:C.964 ZN.17: 4 residues within 4Å: Chain I: C.737, C.740, C.775, C.778 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.740 ZN.18: 4 residues within 4Å: Chain I: C.785, C.788, H.835, H.838 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.785, I:C.788, I:H.835, I:H.838 ZN.19: 5 residues within 4Å: Chain I: C.827, C.830, C.856, C.858 Ligands: ZN.20 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.827, I:C.830, I:C.856, I:C.858 ZN.20: 6 residues within 4Å: Chain I: C.830, H.832, C.849, C.854, C.856 Ligands: ZN.19 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.830, I:C.849, I:C.854 ZN.21: 4 residues within 4Å: Chain J: C.737, C.740, C.775, C.778 No protein-ligand interaction detected (PLIP) ZN.22: 6 residues within 4Å: Chain J: C.785, L.787, C.788, G.834, H.835, H.838 No protein-ligand interaction detected (PLIP) ZN.23: 4 residues within 4Å: Chain J: N.829, C.830, C.856, C.858 No protein-ligand interaction detected (PLIP) ZN.24: 3 residues within 4Å: Chain J: C.830, H.832, C.849 No protein-ligand interaction detected (PLIP) ZN.25: 4 residues within 4Å: Chain K: C.722, C.733, C.736, H.737 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.722, K:C.733, K:C.736 ZN.26: 2 residues within 4Å: Chain K: C.746, H.768 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.746, K:H.768, K:H.768 ZN.27: 5 residues within 4Å: Chain K: C.757, C.760, S.761, H.762, C.787 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.757, K:C.760, K:C.787 ZN.28: 4 residues within 4Å: Chain K: C.760, H.762, C.779, C.783 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:H.762, K:C.783 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: 4 residues within 4Å: Chain L: C.938, 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, T.962, C.964 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: ABIJ
GATOR2 complex protein WDR24: CK
GATOR2 complex protein WDR59: DL
Isoform B of Nucleoporin SEH1: EFGMNO
Protein SEC13 homolog: HP
Sestrin-2: QR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

I
K

J
L

C
C

K
M

D
D

L
N

E
E

F
F

G
G

M
O

N
P

O
Q

H
H

P
R

Q
U

R
V

GATOR2 complex protein MIOS

GATOR2 complex protein WDR24

GATOR2 complex protein WDR59

Isoform B of Nucleoporin SEH1

Protein SEC13 homolog

Sestrin-2

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