SMTL ID : 6msb.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain I: E.51, H.112, H.114, D.125 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.51, 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, 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, R.346 Ligands: MG.3 15 PLIP interactions: 10 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 Salt bridges: M:K.222, M:K.222, N:R.343, N:R.343, N:R.343, N:R.346 ATP.4: 17 residues within 4Å: Chain N: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, H.368, G.392, A.393, K.396 Chain O: R.299, R.302 Ligands: MG.5 14 PLIP interactions: 3 interactions with chain O, 11 interactions with chain N Hydrogen bonds: O:R.302, N:G.188, N:G.229, N:T.230, N:G.231, N:K.232, N:T.233, N:T.233, N:T.233, N:L.234 Salt bridges: O:R.299, O:R.299, N:K.232, N:K.232 ATP.7: 16 residues within 4Å: Chain P: D.166, I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, G.372, A.373, N.376 Chain Q: R.305, R.308 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain P, 4 interactions with chain Q Hydrogen bonds: P:D.166, P:G.168, P:G.209, P:C.210, P:G.211, P:K.212, P:T.213, P:T.213, P:T.213, P:M.214, P:N.376 Salt bridges: P:K.212, P:K.212, Q:R.305, Q:R.305, Q:R.305, Q:R.308 ATP.9: 20 residues within 4Å: Chain Q: E.148, I.149, G.150, L.152, P.190, G.191, T.192, G.193, K.194, T.195, L.196, E.248, N.294, I.326, H.330, G.354, A.355 Chain R: R.344, R.347 Ligands: MG.10 18 PLIP interactions: 14 interactions with chain Q, 4 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:E.248, Q:E.248, Q:N.294 Salt bridges: Q:K.194, Q:K.194, R:R.344, R:R.344, R:R.344, R:R.347

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: 2 residues within 4Å: Chain N: T.233 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.233 MG.8: 2 residues within 4Å: Chain P: T.213 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.213 MG.10: 2 residues within 4Å: Chain Q: T.195 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.195 MG.12: 3 residues within 4Å: Chain R: T.234, D.286 Ligands: ADP.11 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:T.234, R:D.286, R:D.286

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

ADP.6: 13 residues within 4Å: Chain O: M.142, G.144, L.146, P.184, G.185, T.186, G.187, K.188, T.189, L.190, I.320, G.348, K.352 9 PLIP interactions: 9 interactions with chain O Hydrogen bonds: O:G.144, O:G.144, O:G.185, O:T.186, O:G.187, O:K.188, O:T.189, O:T.189, O:L.190 ADP.11: 16 residues within 4Å: Chain M: R.333 Chain R: D.187, I.188, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, G.393, K.397 Ligands: MG.12 11 PLIP interactions: 9 interactions with chain R, 2 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:K.397, R:K.397 Salt bridges: R:K.233, M:R.333, M:R.333

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

2018-12-05

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: ST
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
w

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

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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