SMTL ID : 9lvk.1

Cryo-EM structure of CASTOR1 bound human GATOR2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.59 Å

Oligo State

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

Ligands

31 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: 5 residues within 4Å: Chain A: C.827, C.830, C.856, C.858 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.827, A:C.830, A:C.856, A:C.858 ZN.4: 5 residues within 4Å: Chain A: C.830, H.832, C.849, C.854 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.830, A:H.832, A:C.849, A:C.854 ZN.5: 4 residues within 4Å: Chain B: C.719, C.722, C.733, C.736 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.719, B:C.722, B:C.733, B:C.736 ZN.6: 4 residues within 4Å: Chain B: C.743, C.746, H.765, H.768 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.743, B:C.746, B:H.765, B:H.768 ZN.7: 4 residues within 4Å: Chain B: C.757, C.760, H.785, C.787 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.757, B:C.760, B:H.785, B:C.787 ZN.8: 4 residues within 4Å: Chain B: C.760, H.762, C.779, C.783 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.760, B:H.762, B:C.779, B:C.783 ZN.9: 5 residues within 4Å: Chain C: C.924, I.926, C.927, H.946, H.949 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.924, C:C.927, C:H.946, C:H.949 ZN.10: 4 residues within 4Å: Chain C: C.938, C.941, C.966, C.968 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.938, C:C.941, C:C.966, C:C.968 ZN.11: 5 residues within 4Å: Chain C: C.941, H.943, C.960, T.962, C.964 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.943, C:C.960, C:C.964 ZN.12: 4 residues within 4Å: Chain H: C.737, C.740, C.775, C.778 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.737, H:C.740, H:C.775, H:C.778 ZN.13: 4 residues within 4Å: Chain H: C.785, C.788, H.835, H.838 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.785, H:C.788, H:H.835, H:H.838 ZN.14: 5 residues within 4Å: Chain H: C.827, C.830, C.856, C.858 Ligands: ZN.15 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.827, H:C.830, H:C.856, H:C.858 ZN.15: 5 residues within 4Å: Chain H: C.830, H.832, C.849, C.854 Ligands: ZN.14 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.830, H:H.832, H:C.849, H:C.854 ZN.16: 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.17: 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.18: 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.19: 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.20: 4 residues within 4Å: Chain J: C.902, C.905, C.914, C.917 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.902, J:C.905, J:C.914, J:C.917 ZN.21: 4 residues within 4Å: Chain J: C.924, C.927, H.946, H.949 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.924, J:C.927, J:H.946, J:H.949 ZN.22: 5 residues within 4Å: Chain J: C.938, C.941, C.966, C.968 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.938, J:C.941, J:C.966, J:C.968 ZN.23: 6 residues within 4Å: Chain J: C.941, H.943, C.960, C.964, C.966 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.941, J:H.943, J:C.960, J:C.964 ZN.24: 4 residues within 4Å: Chain Q: C.737, C.740, C.775, C.778 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:C.740 ZN.25: 4 residues within 4Å: Chain Q: C.785, C.788, H.835, H.838 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.785, Q:C.788, Q:H.835, Q:H.838 ZN.26: 4 residues within 4Å: Chain Q: C.827, C.830, C.856, C.858 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:C.827, Q:C.830, Q:C.856 ZN.27: 5 residues within 4Å: Chain Q: C.830, H.832, C.849, V.851, C.854 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:H.832, Q:C.849, Q:C.854 ZN.28: 3 residues within 4Å: Chain R: C.737, F.739, C.740 No protein-ligand interaction detected (PLIP) ZN.29: 6 residues within 4Å: Chain R: C.785, L.787, C.788, L.789, H.835, H.838 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.785, R:C.788, R:H.835, R:H.838 ZN.30: 4 residues within 4Å: Chain R: C.827, C.830, C.856, C.858 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.827, R:C.856, R:C.858 ZN.31: 4 residues within 4Å: Chain R: C.830, H.832, C.849, C.854 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:H.832, R:C.849

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: AHQR
GATOR2 complex protein WDR24: BI
GATOR2 complex protein WDR59: CJ
Isoform B of Nucleoporin SEH1: DEFKLM
Isoform 3 of Protein SEC13 homolog: GN
Cytosolic arginine sensor for mTORC1 subunit 1: OP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
K

Q
L

R
B

B
C

I
M

C
D

J
N

D
E

E
F

F
G

K
O

L
P

M
Q

G
H

N
R

O
U

P
V

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

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