SMTL ID : 9ug9.1

The cryo-EM structure of 26S proteasome-Midnolin complex MB state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 16 residues within 4Å: Chain F: E.134, G.136, P.176, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316, G.340, A.341, R.344 Chain L: S.345, R.347 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain L Hydrogen bonds: F:G.136, F:G.136, F:G.177, F:T.178, F:G.179, F:K.180, F:T.181, F:T.181, F:T.181, F:L.182, L:R.347 Salt bridges: F:K.180, L:R.347 ADP.2: 13 residues within 4Å: Chain G: D.186, I.187, G.188, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.188, G:T.233, G:L.234

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

ATP.3: 15 residues within 4Å: Chain F: R.291, R.294 Chain K: G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, I.348, G.372, A.373, N.376 16 PLIP interactions: 11 interactions with chain K, 5 interactions with chain F Hydrogen bonds: K:G.168, K:G.168, K:G.209, K:C.210, K:G.211, K:K.212, K:T.213, K:T.213, K:N.376, F:D.265 Salt bridges: K:K.212, K:K.212, F:R.291, F:R.291, F:R.291, F:R.294 ATP.4: 18 residues within 4Å: Chain L: D.187, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, E.287, N.333, I.365, H.369, G.393, A.394, K.397 Chain R: R.333, R.336 14 PLIP interactions: 10 interactions with chain L, 4 interactions with chain R Hydrogen bonds: L:G.189, L:G.232, L:K.233, L:T.234, L:T.234, L:L.235, L:N.333, L:K.397 Salt bridges: L:K.233, L:K.233, R:R.333, R:R.333, R:R.333, R:R.336 ATP.5: 19 residues within 4Å: Chain G: D.317, R.343, R.346 Chain R: D.176, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, I.354, I.357, H.358, G.382, A.383, R.386 16 PLIP interactions: 12 interactions with chain R, 4 interactions with chain G Hydrogen bonds: R:G.178, R:G.219, R:T.220, R:G.221, R:K.222, R:T.223, R:T.223, R:L.224, R:E.276, R:G.382 Salt bridges: R:K.222, R:K.222, G:R.343, G:R.343, G:R.343, G:R.346

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: G.106 Chain k: E.52, H.113, H.115, D.126 5 PLIP interactions: 5 interactions with chain k Metal complexes: k:E.52, k:H.113, k:H.115, k:D.126, k:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H.Y. et al., The cryo-EM structure of 26S proteasome-Midnolin complex MB state. To Be Published

Release Date

2025-09-10

Peptides

Midnolin: A
26S proteasome non-ATPase regulatory subunit 8: B
Proteasome subunit alpha type-3: C6
Proteasome subunit beta type-5: DS
Proteasome subunit beta type-6: Ea
26S proteasome regulatory subunit 10B: F
26S proteasome regulatory subunit 4: G
26S proteasome complex subunit SEM1: H
Proteasome subunit beta type-7: Ie
Proteasome subunit beta type-1: JU
26S proteasome regulatory subunit 6B: K
26S proteasome regulatory subunit 6A: L
Proteasome subunit beta type-3: Mg
26S proteasome non-ATPase regulatory subunit 1: N
26S proteasome regulatory subunit 8: O
Proteasome subunit alpha type-6: P2
Proteasome subunit beta type-2: Qi
26S proteasome regulatory subunit 7: R
26S proteasome non-ATPase regulatory subunit 3: T
Proteasome subunit beta type-4: VY
Substrate: W
26S proteasome non-ATPase regulatory subunit 12: X
Proteasome subunit alpha type-2: Z4
26S proteasome non-ATPase regulatory subunit 2: 0
26S proteasome non-ATPase regulatory subunit 11: 1
Proteasome subunit alpha type-4: 38
26S proteasome non-ATPase regulatory subunit 6: 5
Proteasome subunit alpha type-7: 7c
26S proteasome non-ATPase regulatory subunit 7: 9
Proteasome subunit alpha type-5: bj
26S proteasome non-ATPase regulatory subunit 13: d
Proteasome subunit alpha type-1: fl
26S proteasome non-ATPase regulatory subunit 4: h
26S proteasome non-ATPase regulatory subunit 14: k

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
u

B
d

C
m

6
M

D
R

S
r

E
n

a
N

F
E

G
B

H
e

I
o

e
O

J
S

U
s

K
D

L
F

M
p

g
P

N
U

O
C

P
G

2
g

Q
q

i
Q

R
A

T
V

V
T

Y
t

W
v

X
W

Z
H

4
h

0
f

1
X

3
I

8
i

5
Y

7
J

c
j

9
Z

b
K

j
k

d
a

f
L

l
l

h
b

k
c

Midnolin

26S proteasome non-ATPase regulatory subunit 8

Proteasome subunit alpha type-3

Proteasome subunit beta type-5

Proteasome subunit beta type-6

26S proteasome regulatory subunit 10B

26S proteasome regulatory subunit 4

26S proteasome complex subunit SEM1

Proteasome subunit beta type-7

Proteasome subunit beta type-1

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 6A

Proteasome subunit beta type-3

26S proteasome non-ATPase regulatory subunit 1

26S proteasome regulatory subunit 8

Proteasome subunit alpha type-6

Proteasome subunit beta type-2

26S proteasome regulatory subunit 7

26S proteasome non-ATPase regulatory subunit 3

Proteasome subunit beta type-4

Substrate

26S proteasome non-ATPase regulatory subunit 12

Proteasome subunit alpha type-2

26S proteasome non-ATPase regulatory subunit 2

26S proteasome non-ATPase regulatory subunit 11

Proteasome subunit alpha type-4

26S proteasome non-ATPase regulatory subunit 6

Proteasome subunit alpha type-7

26S proteasome non-ATPase regulatory subunit 7

Proteasome subunit alpha type-5

26S proteasome non-ATPase regulatory subunit 13

Proteasome subunit alpha type-1

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 14

Related Entries With Identical Sequence