SMTL ID : 6mse.1

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain I: E.51, H.112, H.114, S.122, D.125 Chain S: G.76 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain S Metal complexes: I:E.51, I:H.114, I:S.122, I:D.125, S:G.76

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

ATP.2: 16 residues within 4Å: Chain M: D.176, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, N.322, I.354, H.358, G.382, A.383 Chain N: R.343 Ligands: MG.3 16 PLIP interactions: 13 interactions with chain M, 3 interactions with chain N Hydrogen bonds: M:G.178, M:G.219, M:T.220, M:G.221, M:K.222, M:T.223, M:T.223, M:L.224, M:N.322, M:N.322, M:G.382 Salt bridges: M:K.222, M:K.222, N:R.343, N:R.343, N:R.343 ATP.5: 16 residues within 4Å: Chain P: 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 Q: D.279, R.305, R.308 Ligands: MG.6 14 PLIP interactions: 11 interactions with chain P, 3 interactions with chain Q Hydrogen bonds: P:G.168, P:G.168, P:G.209, P:G.209, P:C.210, P:G.211, P:K.212, P:T.213, P:N.376 Salt bridges: P:K.212, P:K.212, Q:R.305, Q:R.305, Q:R.308 ATP.8: 19 residues within 4Å: Chain M: R.333, R.336 Chain R: D.187, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.9 15 PLIP interactions: 11 interactions with chain R, 4 interactions with chain M Hydrogen bonds: R:G.189, R:G.189, R:G.232, R:K.233, R:T.234, R:L.235, R:N.333, R:N.333, R:K.397 Salt bridges: R:K.233, R:K.233, M:R.333, M:R.333, M:R.333, M:R.336

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain M: T.223, E.276 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.223 MG.6: 4 residues within 4Å: Chain P: T.213 Chain Q: D.279, R.308 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.213 MG.9: 3 residues within 4Å: Chain R: T.234, D.286 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.234

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

ADP.4: 14 residues within 4Å: Chain N: D.186, I.187, G.188, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.188, N:G.188, N:G.229, N:G.231, N:K.232, N:T.233, N:T.233, N:L.234, N:K.396, N:K.396 Salt bridges: N:K.232, N:K.232 ADP.7: 16 residues within 4Å: Chain Q: G.150, L.152, P.189, P.190, G.191, T.192, G.193, K.194, T.195, L.196, I.326, H.330, G.354, A.355, R.358 Chain R: R.344 13 PLIP interactions: 11 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: Q:G.150, Q:G.150, Q:G.191, Q:T.192, Q:G.193, Q:K.194, Q:T.195, Q:T.195, Q:L.196, Q:R.358 Salt bridges: Q:K.194, R:R.344, R:R.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, Y. et al., Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Nature (2019)

Release Date

2018-11-21

Peptides

26S proteasome non-ATPase regulatory subunit 1: A
26S proteasome non-ATPase regulatory subunit 3: B
26S proteasome non-ATPase regulatory subunit 12: C
26S proteasome non-ATPase regulatory subunit 11: D
26S proteasome non-ATPase regulatory subunit 6: E
26S proteasome non-ATPase regulatory subunit 7: F
26S proteasome non-ATPase regulatory subunit 13: G
26S proteasome non-ATPase regulatory subunit 4: H
26S proteasome non-ATPase regulatory subunit 14: I
26S proteasome non-ATPase regulatory subunit 8: J
26S proteasome complex subunit SEM1: K
26S proteasome non-ATPase regulatory subunit 2: L
26S proteasome regulatory subunit 7: M
26S proteasome regulatory subunit 4: N
26S proteasome regulatory subunit 8: O
26S proteasome regulatory subunit 6B: P
26S proteasome regulatory subunit 10B: Q
26S proteasome regulatory subunit 6A: R
Ubiquitin: S
substrate: T
Proteasome subunit alpha type-6: U8
Proteasome subunit alpha type-2: V9
Proteasome subunit alpha type-4: Wa
Proteasome subunit alpha type-7: Xb
Proteasome subunit alpha type-5: Yc
Proteasome subunit alpha type-1: Zd
Proteasome subunit alpha type-3: 0e
Proteasome subunit beta type-6: 1f
Proteasome subunit beta type-7: 2g
Proteasome subunit beta type-3: 3h
Proteasome subunit beta type-2: 4i
Proteasome subunit beta type-5: 5j
Proteasome subunit beta type-1: 6k
Proteasome subunit beta type-4: 7l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
V

C
W

D
X

E
Y

F
Z

G
a

H
b

I
c

J
d

K
e

L
f

M
A

N
B

O
C

P
D

Q
E

R
F

S
u

T
v

U
G

8
g

V
H

9
h

W
I

a
i

X
J

b
j

Y
K

c
k

Z
L

d
l

0
M

e
m

1
N

f
n

2
O

g
o

3
P

h
p

4
Q

i
q

5
R

j
r

6
S

k
s

7
T

l
t

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

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 8

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 10B

26S proteasome regulatory subunit 6A

Ubiquitin

substrate

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

Related Entries With Identical Sequence