SMTL ID : 9nkf.1

Structure of human substrate-free 26S proteasome in the presence of ATPgS and MG-132,SA-like state (composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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-mer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: D.176, V.177, G.178, P.217, P.218, 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.2 14 PLIP interactions: 4 interactions with chain B, 10 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 ATP.4: 17 residues within 4Å: Chain B: I.187, G.188, L.190, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 Chain C: R.307, R.310 Ligands: MG.5 14 PLIP interactions: 4 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:R.310, B:G.188, B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, B:K.396 Salt bridges: C:R.307, C:R.307, C:R.307, B:K.232, B:K.232 ATP.7: 16 residues within 4Å: Chain D: D.166, I.167, G.168, G.209, C.210, G.211, K.212, T.213, M.214, E.266, I.344, G.372, N.376 Chain E: D.279, R.305, R.308 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:G.211, D:K.212, D:T.213, D:T.213, D:M.214, D:E.266, D:N.376, E:D.279 Salt bridges: D:K.212, D:K.212, E:R.305, E:R.305, E:R.305, E:R.308 ATP.9: 18 residues within 4Å: Chain E: E.148, I.149, G.150, L.152, G.191, T.192, G.193, K.194, T.195, L.196, N.294, I.326, I.329, H.330, G.354 Ligands: MG.10 Chain i: R.344, R.347 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain i Hydrogen bonds: E:G.150, E:G.150, E:G.191, E:K.194, E:T.195, E:T.195, E:T.195, E:L.196, E:D.247, E:N.294, i:R.347 Salt bridges: i:R.344, i:R.344

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.223, D.275 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.223 MG.3: 4 residues within 4Å: Chain A: P.334, L.337, D.338, K.340 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.338 MG.5: 3 residues within 4Å: Chain B: T.233, D.285 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.8: 5 residues within 4Å: Chain D: E.266 Chain E: M.272, L.275, N.276, R.308 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.266 MG.10: 3 residues within 4Å: Chain E: N.294 Ligands: ATP.9 Chain i: R.347 No protein-ligand interaction detected (PLIP)

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

ADP.6: 12 residues within 4Å: Chain C: G.152, P.191, P.192, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, G.356 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.152, C:G.152, C:T.194, C:G.195, C:K.196, C:T.197, C:L.198 Salt bridges: C:K.196 ADP.18: 14 residues within 4Å: Chain A: D.307, R.333 Chain i: D.187, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, A.394 15 PLIP interactions: 11 interactions with chain i, 4 interactions with chain A Hydrogen bonds: i:G.189, i:G.189, i:T.231, i:G.232, i:K.233, i:T.234, i:T.234, i:T.234, i:L.235, i:K.397, A:D.307, A:R.336 Salt bridges: i:K.233, A:R.333, A:R.333

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

LDZ.11: 21 residues within 4Å: Chain M: T.35, R.53, T.54, T.55, T.56, A.61, N.62, T.65, K.67, R.79, S.80, G.81, S.82, A.83, Q.87, M.129 Chain N: Y.157, H.159, S.161, T.162, D.163 14 PLIP interactions: 10 interactions with chain M, 4 interactions with chain N Hydrophobic interactions: M:T.54, M:A.61, M:N.62, M:A.83, N:Y.157, N:Y.157, N:H.159, N:D.163 Hydrogen bonds: M:T.35, M:T.55, M:T.55, M:T.55, M:G.81, M:A.83 LDZ.12: 20 residues within 4Å: Chain N: T.44, R.62, A.63, T.64, E.65, G.66, A.70, K.76, G.88, A.89, G.90, T.91, A.92, T.95 Chain O: D.125, L.126, I.127, C.129, M.131 Chain R: F.61 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:A.63, N:K.76 Hydrogen bonds: N:T.64, N:T.64, N:T.64, N:G.90, N:A.92 LDZ.13: 17 residues within 4Å: Chain Q: 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 g: D.153, P.154, S.157 11 PLIP interactions: 10 interactions with chain Q, 1 interactions with chain g Hydrophobic interactions: Q:A.79, Q:A.86, Q:V.90, Q:A.108, g:D.153 Hydrogen bonds: Q:T.80, Q:T.80, Q:K.92, Q:G.106, Q:G.106, Q:A.108 LDZ.15: 19 residues within 4Å: Chain b: T.35, R.53, T.54, T.55, T.56, A.61, T.65, K.67, R.79, S.80, G.81, S.82, A.83, T.86, M.129, S.203 Chain c: Y.157, H.159, S.161 8 PLIP interactions: 6 interactions with chain b, 2 interactions with chain c Hydrophobic interactions: b:A.61, b:K.67, c:Y.157, c:Y.157 Hydrogen bonds: b:T.55, b:T.55, b:G.81, b:A.83 LDZ.16: 20 residues within 4Å: Chain c: T.44, R.62, A.63, T.64, E.65, G.66, A.70, C.74, K.76, H.78, G.88, A.89, G.90, T.91, A.92, T.95 Chain d: I.127, C.129, M.131 Chain g: F.61 9 PLIP interactions: 9 interactions with chain c Hydrophobic interactions: c:K.76 Hydrogen bonds: c:T.44, c:T.64, c:T.64, c:T.64, c:K.76, c:G.90, c:T.91, c:A.92 LDZ.17: 24 residues within 4Å: Chain R: S.151, F.152, D.153, P.154, V.155, S.157, Y.158, Q.159 Chain f: T.60, R.78, A.79, T.80, A.81, G.82, A.86, V.90, K.92, M.104, A.105, G.106, G.107, A.108, S.155, Y.228 9 PLIP interactions: 2 interactions with chain R, 7 interactions with chain f Hydrophobic interactions: R:V.155, R:Q.159, f:A.79, f:M.104, f:A.108 Hydrogen bonds: f:T.80, f:T.80, f:K.92, f:G.106

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain 0: E.52, H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:E.52, 0:H.113, 0:H.115, 0:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peddada, N. et al., Structure of human substrate-free 26S proteasome in the presence of ATPgS and MG-132,SA-like 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
Proteasome subunit alpha type-6: F4
Proteasome subunit alpha type-2: G5
Proteasome subunit alpha type-4: H6
Proteasome subunit alpha type-7: I7
Proteasome subunit alpha type-5: J8
Proteasome subunit alpha type-1: K9
Proteasome subunit alpha type-3: La
Proteasome subunit beta type-6: Mb
Proteasome subunit beta type-7: Nc
Proteasome subunit beta type-3: Od
Proteasome subunit beta type-2: Pe
Proteasome subunit beta type-5: Qf
Proteasome subunit beta type-1: Rg
Proteasome subunit beta type-4: Sh
26S proteasome non-ATPase regulatory subunit 3: T
26S proteasome non-ATPase regulatory subunit 12: U
26S proteasome non-ATPase regulatory subunit 11: V
26S proteasome non-ATPase regulatory subunit 6: W
26S proteasome non-ATPase regulatory subunit 7: X
26S proteasome non-ATPase regulatory subunit 13: Y
26S proteasome non-ATPase regulatory subunit 4: Z
26S proteasome non-ATPase regulatory subunit 14: 0
26S proteasome non-ATPase regulatory subunit 8: 1
26S proteasome complex subunit SEM1: 2
26S proteasome non-ATPase regulatory subunit 2: 3
26S proteasome regulatory subunit 6A: i
26S proteasome non-ATPase regulatory subunit 1: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

4
g

G
H

5
h

H
I

6
i

I
J

7
j

J
K

8
k

K
L

9
l

L
M

a
m

M
N

b
n

N
O

c
o

O
P

d
p

P
Q

e
q

Q
R

f
r

R
S

g
s

S
T

h
t

T
V

U
W

V
X

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

i
F

j
U

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

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 14

26S proteasome non-ATPase regulatory subunit 8

26S proteasome complex subunit SEM1

26S proteasome non-ATPase regulatory subunit 2

26S proteasome regulatory subunit 6A

26S proteasome non-ATPase regulatory subunit 1

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