SMTL ID : 6msk.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain I: H.112, H.114, D.125 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:H.112, I:H.114, I:H.114, I:D.125, I:D.125

4 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, I.354, H.358, G.382, A.383 Chain N: D.317, R.343 Ligands: MG.3 13 PLIP interactions: 8 interactions with chain M, 5 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, N:D.317, N:R.346 Salt bridges: N:R.343, 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 14 PLIP interactions: 10 interactions with chain N, 4 interactions with chain O Hydrogen bonds: N:G.188, N:G.229, N:T.230, N:G.231, N:K.232, N:T.233, N:T.233, N:L.234, N:N.332 Salt bridges: N:K.232, O:R.299, O:R.299, O:R.299, O:R.302 ATP.6: 17 residues within 4Å: Chain O: M.142, I.143, P.184, G.185, T.186, G.187, K.188, T.189, L.190, E.242, I.320, H.324, A.349, K.352 Chain P: R.323, R.326 Ligands: MG.7 12 PLIP interactions: 4 interactions with chain P, 8 interactions with chain O Salt bridges: P:R.323, P:R.323, P:R.323, P:R.326, O:K.188 Hydrogen bonds: O:I.143, O:G.185, O:T.186, O:G.187, O:K.188, O:T.189, O:L.190 ATP.10: 19 residues within 4Å: Chain M: R.333, R.336 Chain R: D.187, I.188, 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 Ligands: MG.11 15 PLIP interactions: 3 interactions with chain M, 12 interactions with chain R Salt bridges: M:R.333, M:R.333, M:R.336, R:K.233, R:K.233 Hydrogen bonds: R:G.189, R:G.189, R:T.231, R:G.232, R:K.233, R:T.234, R:T.234, R:L.235, R:N.333, R:N.333

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain M: T.223 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.223 MG.5: 4 residues within 4Å: Chain N: T.233, D.285, E.286 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.233 MG.7: 4 residues within 4Å: Chain O: T.189, E.242 Chain P: D.297 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.189 MG.9: 2 residues within 4Å: Chain P: T.213 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.213 MG.11: 3 residues within 4Å: Chain R: T.234, D.286 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.234

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

ADP.8: 15 residues within 4Å: Chain P: I.167, G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373, N.376 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain P Hydrogen bonds: P:G.168, P:G.168, P:G.209, P:G.211, P:K.212, P:T.213, P:T.213, P:M.214, P:N.376

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: T7
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

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

7
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

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

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