SMTL ID : 9uf8.1

The cryo-EM structure of 26S proteasome-Midnolin complex in the MA state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 17 residues within 4Å: Chain B: D.187, I.188, G.189, L.191, P.229, T.231, G.232, K.233, T.234, L.235, I.365, H.369, G.393, A.394, K.397 Chain f: R.333, R.336 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain f Hydrogen bonds: B:D.187, B:G.189, B:G.232, B:K.233, B:T.234, B:T.234, B:K.397, f:R.333, f:R.333, f:R.336 Salt bridges: f:R.333 ADP.4: 15 residues within 4Å: Chain i: M.150, G.152, P.192, G.193, T.194, G.195, K.196, T.197, L.198, I.328, I.331, H.332, G.356, A.357, K.360 7 PLIP interactions: 7 interactions with chain i Hydrogen bonds: i:G.152, i:G.193, i:T.194, i:G.195, i:K.196, i:T.197, i:L.198

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

ATP.2: 14 residues within 4Å: Chain f: V.177, G.178, G.179, P.217, G.219, T.220, G.221, K.222, T.223, L.224, I.354, A.383 Chain h: D.317, R.346 11 PLIP interactions: 9 interactions with chain f, 2 interactions with chain h Hydrogen bonds: f:V.177, f:G.178, f:G.219, f:G.221, f:K.222, f:T.223, f:T.223, f:T.223, f:L.224, h:D.317 Salt bridges: h:R.346 ATP.3: 15 residues within 4Å: Chain h: G.229, T.230, G.231, K.232, T.233, L.234, L.235, K.237, I.364, H.368, G.392, A.393, K.396 Chain i: R.307, R.310 16 PLIP interactions: 1 interactions with chain i, 15 interactions with chain h Salt bridges: i:R.310, h:K.232, h:K.232, h:K.237 Hydrogen bonds: h:G.229, h:G.229, h:T.230, h:G.231, h:K.232, h:T.233, h:T.233, h:T.233, h:L.234, h:L.235, h:E.286, h:E.286 ATP.5: 14 residues within 4Å: Chain j: I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373, N.376 Chain k: R.291 14 PLIP interactions: 11 interactions with chain j, 3 interactions with chain k Hydrogen bonds: j:G.168, j:G.168, j:G.209, j:G.211, j:K.212, j:T.213, j:T.213, j:M.214, j:N.376 Salt bridges: j:K.212, j:K.212, k:R.291, k:R.291, k:R.291 ATP.6: 20 residues within 4Å: Chain B: G.319, R.344, R.347 Chain k: E.134, I.135, G.136, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, E.234, I.312, H.316, G.340, A.341, R.344 14 PLIP interactions: 12 interactions with chain k, 2 interactions with chain B Hydrogen bonds: k:G.136, k:G.136, k:G.177, k:T.178, k:T.178, k:G.179, k:K.180, k:T.181, k:T.181, k:T.181, k:L.182, k:E.234 Salt bridges: B:R.344, B:R.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2025-09-10

Peptides

Proteasome subunit beta type-6: A2
26S proteasome regulatory subunit 6A: B
Proteasome subunit beta type-7: C4
Proteasome subunit alpha type-6: DQ
Proteasome subunit beta type-3: E6
Proteasome subunit alpha type-2: FS
Proteasome subunit beta type-2: G8
Proteasome subunit alpha type-4: HO
Proteasome subunit beta type-5: Ia
Proteasome subunit alpha type-7: JU
Proteasome subunit beta type-1: Kc
Proteasome subunit alpha type-5: LW
Proteasome subunit beta type-4: Me
Proteasome subunit alpha type-1: NY
Proteasome subunit alpha type-3: P0
26S proteasome non-ATPase regulatory subunit 1: R
26S proteasome non-ATPase regulatory subunit 3: T
26S proteasome non-ATPase regulatory subunit 12: V
26S proteasome non-ATPase regulatory subunit 11: X
26S proteasome non-ATPase regulatory subunit 6: Z
26S proteasome non-ATPase regulatory subunit 7: 1
26S proteasome non-ATPase regulatory subunit 13: 3
26S proteasome non-ATPase regulatory subunit 4: 5
26S proteasome non-ATPase regulatory subunit 14: 7
26S proteasome non-ATPase regulatory subunit 8: 9
26S proteasome complex subunit SEM1: b
26S proteasome non-ATPase regulatory subunit 2: d
26S proteasome regulatory subunit 7: f
Midnolin: g
26S proteasome regulatory subunit 4: h
26S proteasome regulatory subunit 8: i
26S proteasome regulatory subunit 6B: j
26S proteasome regulatory subunit 10B: k

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

2
n

B
F

C
O

4
o

D
G

Q
g

E
P

6
p

F
H

S
h

G
Q

8
q

H
I

O
i

I
R

a
r

J
J

U
j

K
S

c
s

L
K

W
k

M
T

e
t

N
L

Y
l

P
M

0
m

R
U

T
V

V
W

X
X

Z
Y

1
Z

3
a

5
b

7
c

9
d

b
e

d
f

f
A

g
u

h
B

i
C

j
D

k
E

Proteasome subunit beta type-6

26S proteasome regulatory subunit 6A

Proteasome subunit beta type-7

Proteasome subunit alpha type-6

Proteasome subunit beta type-3

Proteasome subunit alpha type-2

Proteasome subunit beta type-2

Proteasome subunit alpha type-4

Proteasome subunit beta type-5

Proteasome subunit alpha type-7

Proteasome subunit beta type-1

Proteasome subunit alpha type-5

Proteasome subunit beta type-4

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

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

26S proteasome regulatory subunit 7

Midnolin

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 8

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 10B

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