SMTL ID : 6msh.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 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.112, I:H.114, I:H.114, I:D.125

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

ATP.2: 18 residues within 4Å: Chain O: M.142, I.143, G.144, G.185, T.186, G.187, K.188, T.189, L.190, E.242, I.320, I.323, H.324, G.348, A.349, K.352 Chain P: R.323, R.326 11 PLIP interactions: 7 interactions with chain O, 4 interactions with chain P Hydrogen bonds: O:I.143, O:G.187, O:K.188, O:T.189, O:T.189, O:L.190, P:D.297 Salt bridges: O:K.188, P:R.323, P:R.323, P:R.326 ATP.3: 16 residues within 4Å: Chain P: I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, G.372, A.373, N.376 Chain Q: R.305, R.308 15 PLIP interactions: 3 interactions with chain Q, 12 interactions with chain P Hydrogen bonds: Q:R.305, Q:R.308, 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.312, P:N.376 Salt bridges: Q:R.305, P:K.212 ATP.4: 17 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: A.341, R.344 16 PLIP interactions: 4 interactions with chain R, 12 interactions with chain Q Hydrogen bonds: R:R.347, Q:G.150, Q:G.150, Q:G.191, Q:G.191, Q:G.193, Q:K.194, Q:T.195, Q:L.196, Q:G.354, Q:R.358 Salt bridges: R:R.344, R:R.344, R:R.344, Q:K.194, Q:K.194

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

ADP.5: 15 residues within 4Å: Chain R: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, G.393, A.394 7 PLIP interactions: 7 interactions with chain R Hydrogen bonds: R:G.189, R:G.189, R:G.230, R:G.232, R:K.233, R:T.234, R:T.234

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
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

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

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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