SMTL ID : 9bv3.1

M1B Midnolin-Proteasome

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

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

ATP.1: 22 residues within 4Å: Chain M: D.176, V.177, G.178, P.217, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, N.322, I.354, H.358, G.382, A.383, R.386 Chain N: D.317, R.343, R.346 Ligands: MG.2 18 PLIP interactions: 14 interactions with chain M, 4 interactions with chain N Hydrogen bonds: M:G.178, M:G.178, M:P.217, M:G.219, M:T.220, M:G.221, M:K.222, M:T.223, M:L.224, M:E.276, M:N.322, M:G.382 Salt bridges: M:K.222, M:K.222, N:R.343, N:R.343, N:R.343, N:R.346 ATP.6: 21 residues within 4Å: Chain P: I.167, G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, N.312, I.344, I.348, G.372, A.373, N.376 Chain Q: D.265, R.291, R.294 Ligands: MG.7 17 PLIP interactions: 13 interactions with chain P, 4 interactions with chain Q Hydrogen bonds: P:G.168, P:P.207, P:G.209, P:C.210, P:G.211, P:G.211, P:K.212, P:T.213, P:M.214, P:N.312, P:N.376 Salt bridges: P:K.212, P:K.212, Q:R.291, Q:R.291, Q:R.291, Q:R.294 ATP.8: 21 residues within 4Å: Chain Q: E.134, I.135, G.136, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, E.234, N.280, I.312, H.316, G.340, A.341, R.344 Chain R: R.344, R.347 Ligands: MG.9 21 PLIP interactions: 16 interactions with chain Q, 5 interactions with chain R Hydrogen bonds: Q:G.136, Q:P.175, Q:G.177, Q:T.178, Q:T.178, Q:T.178, Q:G.179, Q:G.179, Q:K.180, Q:T.181, Q:L.182, Q:E.234, Q:E.234, Q:N.280, R:R.344 Salt bridges: Q:K.180, Q:K.180, R:R.344, R:R.344, R:R.344, R:R.347 ATP.10: 24 residues within 4Å: Chain M: D.307, R.333, R.336 Chain R: D.187, I.188, G.189, G.190, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, R.238, E.287, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.11 20 PLIP interactions: 4 interactions with chain M, 16 interactions with chain R Salt bridges: M:R.333, M:R.333, M:R.333, M:R.336, R:K.233, R:K.233 Hydrogen bonds: R:G.189, R:G.190, R:G.230, R:T.231, R:G.232, R:K.233, R:T.234, R:L.235, R:R.238, R:E.287, R:E.287, R:N.333, R:K.397, R:K.397

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain M: T.223, D.275, E.276 Chain N: R.346 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.223 MG.4: 4 residues within 4Å: Chain N: T.233, D.285 Chain O: R.310 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.233 MG.7: 3 residues within 4Å: Chain P: T.213 Chain Q: R.294 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.213 MG.9: 3 residues within 4Å: Chain Q: T.181, D.233 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.181 MG.11: 4 residues within 4Å: Chain R: T.234, D.286, E.287 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.234

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

ADP.3: 18 residues within 4Å: Chain N: I.187, G.188, P.227, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 Chain O: R.307, R.310 Ligands: MG.4 14 PLIP interactions: 11 interactions with chain N, 3 interactions with chain O Hydrogen bonds: N:G.188, N:G.188, N:G.229, N:T.230, N:G.231, N:K.232, N:T.233, N:T.233, N:L.234, O:R.310 Salt bridges: N:K.232, N:K.232, O:R.307, O:R.307 ADP.5: 16 residues within 4Å: Chain O: M.150, I.151, G.152, L.154, P.191, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, G.356, A.357, K.360 11 PLIP interactions: 11 interactions with chain O Hydrogen bonds: O:G.152, O:P.191, O:G.193, O:T.194, O:T.194, O:T.194, O:G.195, O:K.196, O:T.197, O:L.198 Salt bridges: O:K.196

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

Midnolin: A
26S proteasome non-ATPase regulatory subunit 1: B
26S proteasome non-ATPase regulatory subunit 3: C
26S proteasome non-ATPase regulatory subunit 12: D
26S proteasome non-ATPase regulatory subunit 11: E
26S proteasome non-ATPase regulatory subunit 6: F
26S proteasome non-ATPase regulatory subunit 7: G
26S proteasome non-ATPase regulatory subunit 13: H
26S proteasome non-ATPase regulatory subunit 4: I
26S proteasome non-ATPase regulatory subunit 14: J
26S proteasome non-ATPase regulatory subunit 8: K
26S proteasome complex subunit SEM1: L
26S proteasome regulatory subunit 7: M
26S proteasome regulatory subunit 4: N
26S protease regulatory subunit 8: O
26S proteasome regulatory subunit 6B: P
26S protease regulatory subunit 10B: Q
26S proteasome regulatory subunit 6A: R
Proteasome subunit alpha type-6: S
Proteasome subunit alpha type-2: T
Proteasome subunit alpha type-4: U
Proteasome subunit alpha type-7: V
Proteasome subunit alpha type-1: W
Proteasome subunit alpha type-3: X
Proteasome subunit beta type-6: Y6
Proteasome subunit beta type-7: Z7
Proteasome subunit beta type-3: 08
Proteasome subunit beta type-2: 19
Proteasome subunit beta type-5: 2a
Proteasome subunit beta type-1: 3b
Proteasome subunit beta type-4: 4c
Proteasome subunit alpha type-5: 5
26S proteasome non-ATPase regulatory subunit 2: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
y

B
U

C
V

D
W

E
X

F
Y

G
Z

H
a

I
b

J
c

K
d

L
e

M
A

N
B

O
C

P
D

Q
E

R
F

S
G

T
H

U
I

V
J

W
L

X
M

Y
N

6
n

Z
O

7
o

0
P

8
p

1
Q

9
q

2
R

a
r

3
S

b
s

4
T

c
t

5
K

d
f

Midnolin

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-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

26S proteasome non-ATPase regulatory subunit 2

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