SMTL ID : 6msj.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain I: H.112, H.114, D.125 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.112, I:H.114, I:D.125, I:D.125

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

ATP.2: 17 residues within 4Å: Chain M: D.176, V.177, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, I.354, H.358, G.382, A.383 Chain N: R.343 Ligands: MG.3 9 PLIP interactions: 7 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:G.219, M:T.220, M:T.220, M:G.221, M:K.222, M:T.223, M:G.382 Salt bridges: N:R.343, N:R.343 ATP.4: 18 residues within 4Å: Chain N: I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, N.332, I.364, H.368, G.392, A.393, K.396 Chain O: R.299, R.302 Ligands: MG.5 18 PLIP interactions: 14 interactions with chain N, 4 interactions with chain O Hydrogen bonds: N:G.188, N:G.229, N:T.230, N:T.230, N:G.231, N:K.232, N:T.233, N:T.233, N:L.234, N:N.332, N:N.332, N:K.396 Salt bridges: N:K.232, N:K.232, O:R.299, O:R.299, O:R.299, O:R.302 ATP.6: 18 residues within 4Å: Chain O: I.143, L.146, G.185, T.186, G.187, K.188, T.189, L.190, E.242, I.320, H.324, G.348, A.349, K.352 Chain P: D.297, R.323, R.326 Ligands: MG.7 12 PLIP interactions: 8 interactions with chain O, 4 interactions with chain P Hydrogen bonds: O:G.144, O:G.187, O:K.188, O:T.189, O:T.189, O:T.189, O:L.190, O:E.242 Salt bridges: P:R.323, P:R.323, P:R.323, P:R.326 ATP.8: 17 residues within 4Å: Chain P: I.167, 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.9 14 PLIP interactions: 10 interactions with chain P, 4 interactions with chain Q Hydrogen bonds: P:G.168, P:G.168, P:G.209, P:C.210, P:G.211, P:K.212, P:T.213, P:T.213, P:M.214, P:N.376 Salt bridges: Q:R.305, Q:R.305, Q:R.305, Q:R.308

4 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.5: 3 residues within 4Å: Chain N: T.233 Chain O: D.273 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.233 MG.7: 3 residues within 4Å: Chain O: T.189, E.242 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain P: T.213 Chain Q: N.276, D.279, R.308 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.213

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

ADP.10: 16 residues within 4Å: Chain Q: E.148, I.149, G.150, 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 11 PLIP interactions: 10 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:G.150, Q:G.150, Q:G.191, Q:T.192, Q:K.194, Q:T.195, Q:T.195, Q:L.196, Q:G.354, Q:R.358 Salt bridges: 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
Rpt2, NP_002793.2 (26SHA chain B): 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
substrate: S
Proteasome subunit alpha type-6: T
Proteasome subunit alpha type-2: U8
Proteasome subunit alpha type-4: V9
Proteasome subunit alpha type-7: Wa
Proteasome subunit alpha type-5: Xb
Proteasome subunit alpha type-1: Yc
Proteasome subunit alpha type-3: Zd
Proteasome subunit beta type-6: 0e
Proteasome subunit beta type-7: 1f
Proteasome subunit beta type-3: 2g
Proteasome subunit beta type-2: 3h
Proteasome subunit beta type-5: 4i
Proteasome subunit beta type-1: 5j
Proteasome subunit beta type-4: 6k
Proteasome subunit alpha type-6: 7

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
v

T
G

U
H

8
h

V
I

9
i

W
J

a
j

X
K

b
k

Y
L

c
l

Z
M

d
m

0
N

e
n

1
O

f
o

2
P

g
p

3
Q

h
q

4
R

i
r

5
S

j
s

6
T

k
t

7
g

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

Rpt2, NP_002793.2 (26SHA chain B)

26S proteasome regulatory subunit 8

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 10B

26S proteasome regulatory subunit 6A

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

Proteasome subunit alpha type-6

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