SMTL ID : 9nkj.1

Structure of substrates-engaged MIDN-bound human 26S proteasome,ED-MIDN state (Composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: unknown density-Substrate density(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 14 residues within 4Å: Chain A: K.248, A.289, E.294 Chain B: K.258, Y.259, L.260, S.299 Chain C: K.222, F.223, I.224 Chain D: K.238, Y.239, L.240 Chain F: D.303 13 PLIP interactions: 1 interactions with chain F, 3 interactions with chain C, 3 interactions with chain D, 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: F:D.303, C:K.222, D:K.238, D:L.240, B:K.258, B:L.260, B:S.299, B:G.300, B:G.301 Hydrophobic interactions: C:F.223, C:I.224, D:L.240, A:A.289

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

ATP.2: 19 residues within 4Å: Chain A: D.176, V.177, G.178, G.179, G.219, T.220, G.221, K.222, T.223, L.224, I.354, I.357, H.358, G.382, R.386 Chain B: D.317, R.343, R.346 Ligands: MG.3 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B 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:R.386, B:D.317 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.343, B:R.346 ATP.4: 16 residues within 4Å: Chain B: I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393 Chain C: D.281, R.307, R.310 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:T.230, B:G.231, B:G.231, B:T.233, B:L.234 Salt bridges: B:K.232, B:K.232, C:R.307, C:R.307, C:R.307, C:R.310 ATP.6: 16 residues within 4Å: Chain C: M.150, G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, G.356 Chain D: D.297, R.323, R.326 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.152, C:G.152, C:T.194, C:G.195, C:G.195, C:T.197 Salt bridges: C:K.196, C:K.196, D:R.323, D:R.323, D:R.323, D:R.326, D:R.326 ATP.8: 15 residues within 4Å: Chain A: D.307, R.333, R.336 Chain F: G.189, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, A.394, K.397 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.189, F:G.230, F:T.231, F:G.232, F:K.233, F:T.234, F:L.235, F:E.287, F:N.333 Salt bridges: A:R.333, A:R.333, A:R.336

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain A: T.223, D.275 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.223 MG.5: 4 residues within 4Å: Chain B: R.249, V.250, F.283 Chain C: F.283 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

ADP.7: 13 residues within 4Å: Chain D: D.166, I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.168, D:P.208, D:C.210, D:G.211, D:K.212, D:T.213, D:M.214 Salt bridges: D:K.212, D:K.212

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain N: V.82, H.113, H.115, W.121, D.126 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:H.113, N:H.115, N:D.126, N:D.126

6 x LDZ: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide(Non-covalent)

LDZ.11: 25 residues within 4Å: Chain 0: Y.157, H.159, S.161, T.162, D.163, L.165 Chain Z: T.35, R.53, T.54, T.55, T.56, G.57, A.61, N.62, T.65, K.67, R.79, S.80, G.81, S.82, A.83, A.84, T.86, Q.87, M.129 12 PLIP interactions: 10 interactions with chain Z, 2 interactions with chain 0 Hydrophobic interactions: Z:T.54, Z:N.62, Z:K.67, Z:R.79, Z:A.83, 0:Y.157, 0:D.163 Hydrogen bonds: Z:T.55, Z:T.55, Z:T.55, Z:G.81, Z:A.83 LDZ.12: 22 residues within 4Å: Chain 0: T.44, R.62, A.63, T.64, E.65, A.70, D.71, K.76, G.88, A.89, G.90, T.91, A.92, T.95, G.211 Chain 1: R.99, P.102, D.125, L.126, I.127, C.129, M.131 6 PLIP interactions: 6 interactions with chain 0 Hydrophobic interactions: 0:E.65, 0:A.70 Hydrogen bonds: 0:T.44, 0:T.44, 0:T.64, 0:G.90 LDZ.13: 20 residues within 4Å: Chain 3: T.60, R.78, A.79, T.80, A.81, A.86, V.90, K.92, M.104, A.105, G.106, G.107, A.108, C.111 Chain i: R.128, P.131, D.153, P.154, V.155, S.157 8 PLIP interactions: 7 interactions with chain 3, 1 interactions with chain i Hydrophobic interactions: 3:A.79, 3:V.90, i:V.155 Hydrogen bonds: 3:T.80, 3:T.80, 3:G.106, 3:G.106, 3:A.108 LDZ.14: 20 residues within 4Å: Chain d: T.35, R.53, T.54, T.55, T.56, G.57, A.61, T.65, K.67, R.79, S.80, G.81, S.82, A.83, T.86, M.129 Chain e: Y.157, P.158, H.159, S.161 12 PLIP interactions: 9 interactions with chain d, 3 interactions with chain e Hydrophobic interactions: d:A.61, d:K.67, d:R.79, d:A.83, e:Y.157, e:Y.157, e:P.158 Hydrogen bonds: d:T.55, d:T.55, d:K.67, d:G.81, d:A.83 LDZ.15: 22 residues within 4Å: Chain e: T.44, R.62, A.63, T.64, E.65, A.70, K.76, H.78, G.88, A.89, G.90, T.91, A.92, T.95, D.96 Chain f: R.99, P.102, D.125, L.126, I.127, C.129, M.131 9 PLIP interactions: 8 interactions with chain e, 1 interactions with chain f Hydrophobic interactions: e:A.63, e:A.70, f:L.126 Hydrogen bonds: e:T.44, e:T.64, e:T.64, e:G.90, e:G.90, e:A.92 LDZ.16: 21 residues within 4Å: Chain 4: D.153, P.154, V.155, S.157, Y.158, Q.159 Chain h: T.60, R.78, A.79, T.80, A.81, A.86, S.87, V.90, K.92, M.104, A.105, G.106, G.107, A.108, C.111 9 PLIP interactions: 8 interactions with chain h, 1 interactions with chain 4 Hydrophobic interactions: h:A.79, h:V.90, h:M.104, h:A.108, 4:Q.159 Hydrogen bonds: h:T.80, h:T.80, h:G.106, h:G.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peddada, N. et al., Structure of substrates-engaged MIDN-bound human 26S proteasome,ED-MIDN state (Composite map). 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
26S proteasome non-ATPase regulatory subunit 1: G
26S proteasome non-ATPase regulatory subunit 3: H
26S proteasome non-ATPase regulatory subunit 11: I
26S proteasome non-ATPase regulatory subunit 6: J
26S proteasome non-ATPase regulatory subunit 7: K
26S proteasome non-ATPase regulatory subunit 13: L
26S proteasome non-ATPase regulatory subunit 4: M
26S proteasome non-ATPase regulatory subunit 14: N
26S proteasome non-ATPase regulatory subunit 8: O
26S proteasome non-ATPase regulatory subunit 2: P
26S proteasome non-ATPase regulatory subunit 12: Q
26S proteasome complex subunit SEM1: R
Proteasome subunit alpha type-6: S6
Proteasome subunit alpha type-2: T7
Proteasome subunit alpha type-4: U8
Proteasome subunit alpha type-7: V9
Proteasome subunit alpha type-5: Wa
Proteasome subunit alpha type-1: Xb
Proteasome subunit alpha type-3: Yc
Proteasome subunit beta type-6: Zd
Proteasome subunit beta type-7: 0e
Proteasome subunit beta type-3: 1f
Proteasome subunit beta type-2: 2g
Proteasome subunit beta type-5: 3h
Proteasome subunit beta type-1: 4i
Proteasome subunit beta type-4: 5j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
U

H
V

I
X

J
Y

K
Z

L
a

M
b

N
c

O
d

P
f

Q
W

R
e

S
G

6
g

T
H

7
h

U
I

8
i

V
J

9
j

W
K

a
k

X
L

b
l

Y
M

c
m

Z
N

d
n

0
O

e
o

1
P

f
p

2
Q

g
q

3
R

h
r

4
S

i
s

5
T

j
t

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

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 3

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 non-ATPase regulatory subunit 2

26S proteasome non-ATPase regulatory subunit 12

26S proteasome complex subunit SEM1

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

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