SMTL ID : 9nkg.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

LDZ.1: 25 residues within 4Å: Chain H: 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 Chain I: Y.157, H.159, S.161, T.162, D.163, L.165 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:T.54, H:N.62, H:K.67, H:R.79, H:A.83, I:Y.157, I:D.163 Hydrogen bonds: H:T.55, H:T.55, H:T.55, H:G.81, H:A.83 LDZ.2: 22 residues within 4Å: Chain I: 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 J: R.99, P.102, D.125, L.126, I.127, C.129, M.131 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:A.70, I:T.91, J:L.126 Hydrogen bonds: I:T.44, I:T.64, I:G.90 LDZ.3: 20 residues within 4Å: Chain 0: R.128, P.131, D.153, P.154, V.155, S.157 Chain L: 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 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain 0 Hydrophobic interactions: L:A.81, L:V.90, 0:V.155 Hydrogen bonds: L:T.80, L:T.80, L:G.106, L:G.106, L:A.108 LDZ.4: 20 residues within 4Å: Chain V: 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 W: Y.157, P.158, H.159, S.161 11 PLIP interactions: 8 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:K.67, V:R.79, V:A.83, W:Y.157, W:Y.157, W:P.158 Hydrogen bonds: V:T.55, V:T.55, V:K.67, V:G.81, V:A.83 LDZ.5: 23 residues within 4Å: Chain 0: F.61 Chain W: 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 X: R.99, P.102, D.125, L.126, I.127, C.129, M.131 9 PLIP interactions: 8 interactions with chain W, 1 interactions with chain X Hydrophobic interactions: W:A.63, W:A.70, X:L.126 Hydrogen bonds: W:T.44, W:T.64, W:T.64, W:G.90, W:G.90, W:A.92 LDZ.6: 20 residues within 4Å: Chain M: D.153, P.154, V.155, S.157, Q.159 Chain Z: 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 10 PLIP interactions: 1 interactions with chain M, 9 interactions with chain Z Hydrophobic interactions: M:Q.159, Z:A.79, Z:S.87, Z:V.90, Z:M.104, Z:A.108 Hydrogen bonds: Z:T.80, Z:T.80, Z:G.106, Z:G.106

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

ATP.7: 26 residues within 4Å: Chain 2: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, R.227, N.322, P.346, I.354, I.357, H.358, G.382, A.383, R.386 Chain 3: D.317, A.340, R.343, G.345, R.346 Ligands: MG.8 16 PLIP interactions: 12 interactions with chain 2, 4 interactions with chain 3 Hydrogen bonds: 2:G.178, 2:G.219, 2:T.220, 2:T.220, 2:G.221, 2:K.222, 2:T.223, 2:L.224, 2:H.358, 2:G.382 Salt bridges: 2:K.222, 2:K.222, 3:R.343, 3:R.343, 3:R.343, 3:R.346 ATP.9: 21 residues within 4Å: Chain 3: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, N.332, P.356, T.360, I.364, I.367, H.368, G.392, A.393, K.396 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain 3 Hydrogen bonds: 3:G.188, 3:G.188, 3:G.229, 3:T.230, 3:G.231, 3:K.232, 3:T.233, 3:L.234, 3:H.368 Salt bridges: 3:K.232, 3:K.232 ATP.12: 25 residues within 4Å: Chain 5: D.166, I.167, G.168, M.170, P.207, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, N.312, I.344, T.347, I.348, G.372, A.373, N.376 Chain 6: D.279, A.302, R.305, R.308 Ligands: MG.11 17 PLIP interactions: 13 interactions with chain 5, 4 interactions with chain 6 Hydrogen bonds: 5:G.168, 5:G.168, 5:G.209, 5:C.210, 5:G.211, 5:K.212, 5:T.213, 5:T.213, 5:M.214, 5:E.266, 5:N.376 Salt bridges: 5:K.212, 5:K.212, 6:R.305, 6:R.305, 6:R.305, 6:R.308 ATP.14: 23 residues within 4Å: Chain 2: D.307, R.333, R.336 Chain 7: 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, I.365, I.368, H.369, G.393, A.394, K.397 Ligands: MG.15 16 PLIP interactions: 12 interactions with chain 7, 4 interactions with chain 2 Hydrogen bonds: 7:G.189, 7:G.189, 7:G.230, 7:T.231, 7:G.232, 7:K.233, 7:T.234, 7:L.235, 7:R.238, 7:H.369 Salt bridges: 7:K.233, 7:K.233, 2:R.333, 2:R.333, 2:R.333, 2:R.336

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain 2: T.223, D.275 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.223 MG.10: 3 residues within 4Å: Chain 3: T.233, D.285 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.233 MG.11: 4 residues within 4Å: Chain 5: T.213, D.265 Chain 6: R.308 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:T.213 MG.15: 3 residues within 4Å: Chain 7: T.234, D.286 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.234

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

ADP.13: 20 residues within 4Å: Chain 6: E.148, I.149, G.150, L.152, G.191, T.192, G.193, K.194, T.195, L.196, R.199, I.326, I.329, H.330, G.354, A.355, R.358 Chain 7: D.318, R.344, R.347 14 PLIP interactions: 12 interactions with chain 6, 2 interactions with chain 7 Hydrogen bonds: 6:G.150, 6:G.150, 6:G.191, 6:T.192, 6:T.192, 6:G.193, 6:K.194, 6:T.195, 6:L.196, 6:H.330, 6:G.354 Salt bridges: 6:K.194, 7:R.344, 7:R.344

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 8 residues within 4Å: Chain j: E.52, H.113, H.115, L.122, S.123, D.126 Chain l: A.104, G.105 5 PLIP interactions: 5 interactions with chain j Metal complexes: j:E.52, j:H.113, j:H.115, j:D.126, j: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. To Be Published

Release Date

2025-05-07

Peptides

Proteasome subunit alpha type-6: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-4: CQ
Proteasome subunit alpha type-7: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-1: FT
Proteasome subunit alpha type-3: GU
Proteasome subunit beta type-6: HV
Proteasome subunit beta type-7: IW
Proteasome subunit beta type-3: JX
Proteasome subunit beta type-2: KY
Proteasome subunit beta type-5: LZ
Proteasome subunit beta type-1: M0
Proteasome subunit beta type-4: N1
26S proteasome regulatory subunit 7: 2
26S proteasome regulatory subunit 4: 3
26S protease regulatory subunit 8: 4
26S proteasome regulatory subunit 6B: 5
26S proteasome regulatory subunit 10B: 6
26S proteasome regulatory subunit 6A: 7
26S proteasome non-ATPase regulatory subunit 3: 8
26S proteasome non-ATPase regulatory subunit 12: 9
26S proteasome non-ATPase regulatory subunit 11: a
26S proteasome non-ATPase regulatory subunit 6: b
26S proteasome non-ATPase regulatory subunit 7: c
26S proteasome non-ATPase regulatory subunit 13: d
26S proteasome non-ATPase regulatory subunit 4: e
26S proteasome non-ATPase regulatory subunit 8: f
26S proteasome complex subunit SEM1: g
unknown density (substrate density): h
26S proteasome non-ATPase regulatory subunit 1: i
26S proteasome non-ATPase regulatory subunit 14: j
26S proteasome non-ATPase regulatory subunit 2: k
Midnolin: l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

O
g

B
H

P
h

C
I

Q
i

D
J

R
j

E
K

S
k

F
L

T
l

G
M

U
m

H
N

V
n

I
O

W
o

J
P

X
p

K
Q

Y
q

L
R

Z
r

M
S

0
s

N
T

1
t

2
A

3
B

4
C

5
D

6
E

7
F

8
V

9
W

a
X

b
Y

c
Z

d
a

e
b

f
d

g
e

h
v

i
U

j
c

k
f

l
z

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 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 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)

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 2

Midnolin

Related Entries With Identical Sequence