SMTL ID : 9nki.1

Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state (Composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 25 residues within 4Å: Chain A: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, R.227, I.354, I.357, H.358, G.382, A.383, R.386 Chain B: L.313, D.317, A.340, R.343, G.345, R.346 Ligands: MG.2 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Salt bridges: B:R.343, B:R.343, B:R.343, B:R.346, A:K.222, A:K.222 Hydrogen bonds: A:G.178, A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:L.224, A:H.358 ATP.3: 20 residues within 4Å: Chain B: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, N.332, T.360, I.364, I.367, H.368, G.392, A.393, K.396 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, B:H.368, B:K.396 Salt bridges: B:K.232, B:K.232 ATP.6: 22 residues within 4Å: Chain D: D.166, I.167, G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, I.348, G.372, A.373, N.376 Chain E: D.279, A.302, R.305, R.308 Ligands: MG.5 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain D Salt bridges: E:R.305, E:R.308 Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:M.214, D:N.376 ATP.8: 24 residues within 4Å: Chain A: D.307, R.333, R.336 Chain F: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, R.238, E.287, N.333, I.365, I.368, H.369, G.393, A.394, K.397 Ligands: MG.9 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain F Salt bridges: A:R.333, A:R.333, A:R.336, F:K.233, F:K.233 Hydrogen bonds: F:G.189, F:G.189, F:G.230, F:T.231, F:G.232, F:K.233, F:T.234, F:L.235, F:N.333, F:H.369

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.222, T.223 Chain B: R.343 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain B: G.229, T.230, K.232, T.233 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain D: K.212, T.213 Chain E: R.308 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain F: T.234, D.286, E.287 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.234

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

ADP.7: 22 residues within 4Å: Chain E: E.148, I.149, G.150, L.152, P.190, G.191, T.192, G.193, K.194, T.195, L.196, R.199, N.294, I.326, I.329, H.330, G.354, A.355, R.358 Chain F: D.318, R.344, R.347 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:G.150, E:G.191, E:T.192, E:T.192, E:G.193, E:K.194, E:T.195, E:L.196, E:H.330, E:R.358 Salt bridges: E:K.194, F:R.344, F:R.344, F:R.347

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 7 residues within 4Å: Chain k: E.52, H.113, H.115, W.121, L.122, D.126, V.144 4 PLIP interactions: 4 interactions with chain k Metal complexes: k:H.113, k:H.113, k:H.115, k:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peddada, N. et al., Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state. To Be Published

Release Date

2025-05-07

Peptides

26S proteasome regulatory subunit 7: A
26S proteasome regulatory subunit 4: B
26S protease regulatory subunit 8: C
26S proteasome regulatory subunit 6B: D
26S proteasome regulatory subunit 10B: E
26S proteasome regulatory subunit 6A: F
Proteasome subunit alpha type-6: G3
Proteasome subunit alpha type-2: H4
Proteasome subunit alpha type-4: I5
Proteasome subunit alpha type-7: J6
Proteasome subunit alpha type-5: K7
Proteasome subunit alpha type-1: L8
Proteasome subunit alpha type-3: M9
Proteasome subunit beta type-6: Na
Proteasome subunit beta type-7: Ob
Proteasome subunit beta type-3: Pc
Proteasome subunit beta type-2: Qd
Proteasome subunit beta type-5: Re
Proteasome subunit beta type-1: Sf
Proteasome subunit beta type-4: Tg
26S proteasome non-ATPase regulatory subunit 3: U
26S proteasome non-ATPase regulatory subunit 12: V
26S proteasome non-ATPase regulatory subunit 11: W
26S proteasome non-ATPase regulatory subunit 6: X
26S proteasome non-ATPase regulatory subunit 7: Y
26S proteasome non-ATPase regulatory subunit 13: Z
26S proteasome non-ATPase regulatory subunit 4: 0
26S proteasome non-ATPase regulatory subunit 8: 1
26S proteasome complex subunit SEM1: 2
Unknown density-substrate density: h
Midnolin: i
26S proteasome non-ATPase regulatory subunit 1: j
26S proteasome non-ATPase regulatory subunit 14: k
26S proteasome non-ATPase regulatory subunit 2: l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

3
g

H
H

4
h

I
I

5
i

J
J

6
j

K
K

7
k

L
L

8
l

M
M

9
m

N
N

a
n

O
O

b
o

P
P

c
p

Q
Q

d
q

R
R

e
r

S
S

f
s

T
T

g
t

U
V

V
W

W
X

X
Y

Y
Z

Z
a

0
b

1
d

2
e

h
v

i
z

j
U

k
c

l
f

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S protease regulatory subunit 8

26S proteasome regulatory subunit 6B

26S proteasome 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 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 8

26S proteasome complex subunit SEM1

Unknown density-substrate density

Midnolin

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 2

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