SMTL ID : 9bv1.1

M2A Midnolin-Proteasome (translocating)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain I: V.82, H.113, H.115, S.123, D.126 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.113, I:H.115, I:D.126, I:D.126

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

ATP.2: 20 residues within 4Å: Chain L: 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 M: R.343, R.346 Ligands: MG.3 17 PLIP interactions: 13 interactions with chain L, 4 interactions with chain M Hydrogen bonds: L:G.178, L:G.219, L:T.220, L:T.220, L:G.221, L:K.222, L:T.223, L:L.224, L:N.322, L:G.382, L:R.386 Salt bridges: L:K.222, L:K.222, M:R.343, M:R.343, M:R.343, M:R.346 ATP.4: 21 residues within 4Å: Chain M: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, N.332, I.364, H.368, G.392, A.393, K.396 Chain N: D.281, R.307, R.310 Ligands: MG.5 22 PLIP interactions: 18 interactions with chain M, 4 interactions with chain N Hydrogen bonds: M:G.188, M:G.188, M:G.229, M:T.230, M:T.230, M:G.231, M:G.231, M:K.232, M:T.233, M:T.233, M:L.234, M:E.286, M:N.332, M:G.392, M:K.396, M:K.396 Salt bridges: M:K.232, M:K.232, N:R.307, N:R.307, N:R.307, N:R.310 ATP.6: 24 residues within 4Å: Chain N: M.150, I.151, G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, R.201, E.250, N.296, I.328, H.332, G.356, A.357, K.360 Chain O: D.297, R.323, R.326, L.327 Ligands: MG.7 16 PLIP interactions: 11 interactions with chain N, 5 interactions with chain O Hydrogen bonds: N:G.152, N:G.193, N:T.194, N:T.194, N:G.195, N:K.196, N:T.197, N:L.198, N:R.201, O:R.326, O:R.326 Salt bridges: N:K.196, N:K.196, O:R.323, O:R.323, O:R.323 ATP.11: 21 residues within 4Å: Chain L: D.307, R.333, R.336 Chain Q: D.187, I.188, G.189, L.191, P.228, P.229, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, G.393, A.394, K.397 19 PLIP interactions: 15 interactions with chain Q, 4 interactions with chain L Hydrogen bonds: Q:G.189, Q:G.189, Q:P.228, Q:G.230, Q:G.232, Q:K.233, Q:T.234, Q:T.234, Q:L.235, Q:N.333, Q:N.333, Q:K.397, Q:K.397 Salt bridges: Q:K.233, Q:K.233, L:R.333, L:R.333, L:R.333, L:R.336

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain L: T.223 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.223 MG.5: 3 residues within 4Å: Chain M: T.233, D.285 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.233 MG.7: 3 residues within 4Å: Chain N: T.197, D.249 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.197 MG.9: 3 residues within 4Å: Chain O: T.213, D.265 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.213

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

ADP.8: 16 residues within 4Å: Chain O: D.166, I.167, G.168, P.207, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373, N.376 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:G.168, O:G.168, O:G.209, O:C.210, O:G.211, O:K.212, O:T.213, O:T.213, O:T.213, O:M.214, O:N.376 Salt bridges: O:K.212 ADP.10: 15 residues within 4Å: Chain P: E.134, I.135, G.136, G.137, G.177, T.178, G.179, K.180, T.181, L.182, I.312, I.315, H.316, N.339, G.340 10 PLIP interactions: 10 interactions with chain P Hydrogen bonds: P:G.136, P:G.137, P:P.176, P:K.180, P:T.181, P:T.181, P:T.181, P:L.182, P:G.340 Salt bridges: P:K.180

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 regulatory subunit 7: L
26S proteasome regulatory subunit 4: M
26S protease regulatory subunit 8: N
26S proteasome regulatory subunit 6B: O
26S protease regulatory subunit 10B: P
26S proteasome regulatory subunit 6A: Q
Proteasome subunit alpha type-6: R
Proteasome subunit alpha type-2: S
Proteasome subunit alpha type-4: T
Proteasome subunit alpha type-7: U
Proteasome subunit alpha type-5: V
Proteasome subunit alpha type-1: W
Proteasome subunit alpha type-3: X
Proteasome subunit beta type-6: Y5
Proteasome subunit beta type-7: Z6
Proteasome subunit beta type-3: 07
Proteasome subunit beta type-2: 18
Proteasome subunit beta type-5: 29
Proteasome subunit beta type-1: 3a
Proteasome subunit beta type-4: 4b
26S proteasome non-ATPase regulatory subunit 2: c
Midnolin: d

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
A

M
B

N
C

O
D

P
E

Q
F

R
G

S
H

T
I

U
J

V
K

W
L

X
M

Y
N

5
n

Z
O

6
o

0
P

7
p

1
Q

8
q

2
R

9
r

3
S

a
s

4
T

b
t

c
f

d
y

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 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-5

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

26S proteasome non-ATPase regulatory subunit 2

Midnolin

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