SMTL ID : 9h5k.1

Cryo-EM structure of the SEAC-EGOC supercomplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

28 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.1098, C.1101, H.1120, C.1123 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1098, A:C.1101, A:H.1120, A:C.1123 ZN.2: 4 residues within 4Å: Chain A: C.1112, C.1115, C.1140, C.1142 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1112, A:C.1115, A:C.1140, A:C.1142 ZN.3: 5 residues within 4Å: Chain A: C.1115, H.1117, C.1134, S.1136, C.1138 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1115, A:H.1117, A:C.1134, A:C.1138 ZN.4: 4 residues within 4Å: Chain C: C.1293, C.1296, H.1315, C.1318 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1293, C:C.1296, C:H.1315, C:C.1318 ZN.5: 4 residues within 4Å: Chain C: C.1246, C.1249, C.1283, C.1286 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1246, C:C.1249, C:C.1283, C:C.1286 ZN.6: 4 residues within 4Å: Chain C: C.1310, H.1312, C.1331, C.1335 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1310, C:H.1312, C:C.1331, C:C.1335 ZN.7: 4 residues within 4Å: Chain F: C.953, C.956, H.1013, H.1016 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.953, F:C.956, F:H.1013, F:H.1016 ZN.8: 4 residues within 4Å: Chain F: C.881, C.884, C.943, C.946 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.881, F:C.884, F:C.943, F:C.946 ZN.9: 4 residues within 4Å: Chain F: C.1005, C.1008, C.1034, C.1036 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.1005, F:C.1008, F:C.1034, F:C.1036 ZN.10: 5 residues within 4Å: Chain F: C.1008, H.1010, C.1027, T.1029, C.1032 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.1008, F:H.1010, F:C.1027, F:C.1032 ZN.11: 5 residues within 4Å: Chain G: C.881, C.884, C.943, C.946, S.948 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.881, G:C.884, G:C.943, G:C.946 ZN.12: 4 residues within 4Å: Chain G: C.1005, C.1008, C.1034, C.1036 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.1005, G:C.1008, G:C.1034, G:C.1036 ZN.13: 4 residues within 4Å: Chain G: C.953, C.956, H.1013, H.1016 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.953, G:C.956, G:H.1013, G:H.1016 ZN.14: 5 residues within 4Å: Chain G: C.1008, H.1010, C.1027, T.1029, C.1032 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.1008, G:H.1010, G:C.1027, G:C.1032 ZN.15: 4 residues within 4Å: Chain I: C.1098, C.1101, H.1120, C.1123 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.1098, I:C.1101, I:H.1120, I:C.1123 ZN.16: 4 residues within 4Å: Chain I: C.1112, C.1115, C.1140, C.1142 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.1112, I:C.1115, I:C.1140, I:C.1142 ZN.17: 5 residues within 4Å: Chain I: C.1115, H.1117, C.1134, S.1136, C.1138 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.1115, I:H.1117, I:C.1134, I:C.1138 ZN.18: 4 residues within 4Å: Chain K: C.1293, C.1296, H.1315, C.1318 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.1293, K:C.1296, K:H.1315, K:C.1318 ZN.19: 4 residues within 4Å: Chain K: C.1246, C.1249, C.1283, C.1286 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.1246, K:C.1249, K:C.1283, K:C.1286 ZN.20: 4 residues within 4Å: Chain K: C.1310, H.1312, C.1331, C.1335 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.1310, K:H.1312, K:C.1331, K:C.1335 ZN.21: 4 residues within 4Å: Chain N: C.953, C.956, H.1013, H.1016 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.953, N:C.956, N:H.1013, N:H.1016 ZN.22: 4 residues within 4Å: Chain N: C.881, C.884, C.943, C.946 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.881, N:C.884, N:C.943, N:C.946 ZN.23: 4 residues within 4Å: Chain N: C.1005, C.1008, C.1034, C.1036 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.1005, N:C.1008, N:C.1034, N:C.1036 ZN.24: 5 residues within 4Å: Chain N: C.1008, H.1010, C.1027, T.1029, C.1032 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.1008, N:H.1010, N:C.1027, N:C.1032 ZN.25: 5 residues within 4Å: Chain O: C.881, C.884, C.943, C.946, S.948 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.881, O:C.884, O:C.943, O:C.946 ZN.26: 4 residues within 4Å: Chain O: C.1005, C.1008, C.1034, C.1036 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.1005, O:C.1008, O:C.1034, O:C.1036 ZN.27: 4 residues within 4Å: Chain O: C.953, C.956, H.1013, H.1016 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.953, O:C.956, O:H.1013, O:H.1016 ZN.28: 5 residues within 4Å: Chain O: C.1008, H.1010, C.1027, T.1029, C.1032 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.1008, O:H.1010, O:C.1027, O:C.1032

2 x MG: MAGNESIUM ION(Non-covalent)

MG.29: 5 residues within 4Å: Chain Q: S.20, T.41, D.61 Ligands: AF3.30, GDP.31 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:S.20, Q:T.41, Q:D.61 MG.33: 5 residues within 4Å: Chain Y: S.20, T.41, D.61 Ligands: AF3.34, GDP.35 3 PLIP interactions: 3 interactions with chain Y Metal complexes: Y:S.20, Y:T.41, Y:D.61

2 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.30: 12 residues within 4Å: Chain Q: R.14, S.15, G.16, K.19, A.40, T.41, G.63, G.64, Q.65 Chain S: R.84 Ligands: MG.29, GDP.31 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:G.63 AF3.34: 12 residues within 4Å: Chain 0: R.84 Chain Y: R.14, S.15, G.16, K.19, A.40, T.41, G.63, G.64, Q.65 Ligands: MG.33, GDP.35 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:G.63

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

GDP.31: 21 residues within 4Å: Chain Q: R.14, S.15, G.16, S.17, G.18, K.19, S.20, S.21, T.35, R.36, G.39, H.126, K.127, D.129, L.130, S.165, I.166, W.167 Chain S: R.84 Ligands: MG.29, AF3.30 14 PLIP interactions: 12 interactions with chain Q, 2 interactions with chain S Hydrogen bonds: Q:G.16, Q:S.17, Q:G.18, Q:K.19, Q:S.20, Q:S.21, Q:R.36, Q:K.127, Q:K.127, Q:I.166 Salt bridges: Q:K.19, Q:D.129, S:R.84, S:R.84 GDP.32: 14 residues within 4Å: Chain R: V.17, R.18, R.19, C.20, G.21, K.22, S.23, S.24, H.124, K.125, D.127, S.165, I.166, F.167 10 PLIP interactions: 10 interactions with chain R Hydrogen bonds: R:R.19, R:C.20, R:G.21, R:K.22, R:S.23, R:S.23, R:S.24, R:S.24, R:I.166 Salt bridges: R:D.127 GDP.35: 21 residues within 4Å: Chain 0: R.84 Chain Y: R.14, S.15, G.16, S.17, G.18, K.19, S.20, S.21, T.35, R.36, G.39, H.126, K.127, D.129, L.130, S.165, I.166, W.167 Ligands: MG.33, AF3.34 14 PLIP interactions: 12 interactions with chain Y, 2 interactions with chain 0 Hydrogen bonds: Y:G.16, Y:S.17, Y:G.18, Y:K.19, Y:S.20, Y:S.21, Y:R.36, Y:K.127, Y:K.127, Y:I.166 Salt bridges: Y:K.19, Y:D.129, 0:R.84, 0:R.84 GDP.36: 14 residues within 4Å: Chain Z: V.17, R.18, R.19, C.20, G.21, K.22, S.23, S.24, H.124, K.125, D.127, S.165, I.166, F.167 10 PLIP interactions: 10 interactions with chain Z Hydrogen bonds: Z:R.19, Z:C.20, Z:G.21, Z:K.22, Z:S.23, Z:S.23, Z:S.24, Z:S.24, Z:I.166 Salt bridges: Z:D.127

Links

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Citation

Tafur, L. et al., Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex. To Be Published

Release Date

2025-11-05

Peptides

Maintenance of telomere capping protein 5: AI
Protein transport protein SEC13: BJ
Restriction of telomere capping protein 1: CK
Nucleoporin SEH1: DEHLMP
SEH-associated protein 4: FGNO
GTP-binding protein GTR1: QY
GTP-binding protein GTR2: RZ
Nitrogen permease regulator 2: S0
Nitrogen permease regulator 3: T1
Vacuolar membrane-associated protein IML1: U2
Protein MEH1: V3
Protein EGO2: W4
Protein SLM4: X5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

I
K

B
H

J
P

C
A

K
I

D
F

E
E

H
D

L
N

M
M

P
L

F
G

G
B

N
O

O
J

Q
a

Y
b

R
c

Z
d

S
T

0
g

T
h

1
i

U
X

2
j

V
R

3
S

W
U

4
W

X
Y

5
Z

Maintenance of telomere capping protein 5

Protein transport protein SEC13

Restriction of telomere capping protein 1

Nucleoporin SEH1

SEH-associated protein 4

GTP-binding protein GTR1

GTP-binding protein GTR2

Nitrogen permease regulator 2

Nitrogen permease regulator 3

Vacuolar membrane-associated protein IML1

Protein MEH1

Protein EGO2

Protein SLM4

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