SMTL ID : 9bui.1

M1A Midnolin-Proteasome (with Ubl)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-2-2-2-1-1-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain N: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, N.322, I.354, H.358, G.382, A.383, R.386 Chain O: R.343, R.346 Ligands: MG.2 13 PLIP interactions: 10 interactions with chain N, 3 interactions with chain O Hydrogen bonds: N:G.178, N:G.219, N:T.220, N:G.221, N:K.222, N:T.223, N:T.223, N:L.224, N:N.322 Salt bridges: N:K.222, O:R.343, O:R.343, O:R.346 ATP.5: 16 residues within 4Å: Chain Q: I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, I.344, I.348, G.372, A.373, N.376 Chain R: D.265 14 PLIP interactions: 12 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: Q:G.168, Q:G.209, Q:G.209, Q:G.211, Q:K.212, Q:T.213, Q:T.213, Q:E.266, Q:E.266, Q:N.376, R:D.265, R:D.265 Salt bridges: Q:K.212, Q:K.212 ATP.6: 12 residues within 4Å: Chain R: I.135, P.175, P.176, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316 Chain S: R.347 14 PLIP interactions: 9 interactions with chain R, 5 interactions with chain S Hydrogen bonds: R:P.175, R:G.177, R:T.178, R:G.179, R:K.180, R:T.181, R:L.182, S:K.221, S:K.221 Salt bridges: R:K.180, R:K.180, S:R.347, S:R.347, S:R.347 ATP.7: 17 residues within 4Å: Chain N: A.330, R.333, R.336 Chain S: I.188, G.227, P.229, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, A.394, K.397 14 PLIP interactions: 11 interactions with chain S, 3 interactions with chain N Hydrogen bonds: S:I.188, S:G.230, S:G.232, S:K.233, S:T.234, S:L.235, S:N.333, S:K.397, S:K.397 Salt bridges: S:K.233, S:K.233, N:R.333, N:R.333, N:R.336

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain N: T.223 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.223 MG.4: 4 residues within 4Å: Chain O: K.232, T.233, L.234 Ligands: ADP.3 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 18 residues within 4Å: Chain O: D.186, I.187, G.188, G.189, L.190, P.227, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain O Hydrogen bonds: O:G.188, O:G.189, O:G.229, O:T.230, O:G.231, O:K.232, O:T.233, O:L.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nardone, C. et al., Structural basis for nuclear protein degradation by the midnolin-proteasome pathway. To Be Published

Release Date

2025-06-11

Peptides

26S proteasome non-ATPase regulatory subunit 1: A
26S proteasome non-ATPase regulatory subunit 3: B
26S proteasome non-ATPase regulatory subunit 12: C
26S proteasome non-ATPase regulatory subunit 11: D
26S proteasome non-ATPase regulatory subunit 6: E
26S proteasome non-ATPase regulatory subunit 7: F
26S proteasome non-ATPase regulatory subunit 13: G
26S proteasome non-ATPase regulatory subunit 4: H
26S proteasome non-ATPase regulatory subunit 14: I
26S proteasome non-ATPase regulatory subunit 8: J
26S proteasome complex subunit SEM1: K
26S proteasome non-ATPase regulatory subunit 2: L
Midnolin: M
26S proteasome regulatory subunit 7: N
26S proteasome regulatory subunit 4: O
26S protease regulatory subunit 8: P
26S proteasome regulatory subunit 6B: Q
26S protease regulatory subunit 10B: R
26S proteasome regulatory subunit 6A: S
Proteasome subunit alpha type-6: T
Proteasome subunit alpha type-2: U
Proteasome subunit alpha type-4: V
Proteasome subunit alpha type-7: W
Proteasome subunit alpha type-1: X
Proteasome subunit alpha type-3: Y
Proteasome subunit beta type-6: Z7
Proteasome subunit beta type-7: 08
Proteasome subunit beta type-3: 19
Proteasome subunit beta type-2: 2a
Proteasome subunit beta type-5: 3b
Proteasome subunit beta type-1: 4c
Proteasome subunit beta type-4: 5d
Proteasome subunit alpha type-5: 6
AN1-type zinc finger protein 5: e

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
V

C
W

D
X

E
Y

F
Z

G
a

H
b

I
c

J
d

K
e

L
f

M
y

N
A

O
B

P
C

Q
D

R
E

S
F

T
G

U
H

V
I

W
J

X
L

Y
M

Z
N

7
n

0
O

8
o

1
P

9
p

2
Q

a
q

3
R

b
r

4
S

c
s

5
T

d
t

6
K

e
z

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 3

26S proteasome non-ATPase regulatory subunit 12

26S proteasome non-ATPase regulatory subunit 11

26S proteasome non-ATPase regulatory subunit 6

26S proteasome non-ATPase regulatory subunit 7

26S proteasome non-ATPase regulatory subunit 13

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 8

26S proteasome complex subunit SEM1

26S proteasome non-ATPase regulatory subunit 2

Midnolin

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S protease regulatory subunit 8

26S proteasome regulatory subunit 6B

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

Proteasome subunit alpha type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-5

Proteasome subunit beta type-1

Proteasome subunit beta type-4

Proteasome subunit alpha type-5

AN1-type zinc finger protein 5

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