SMTL ID : 8cvt.1

Human 19S-20S proteasome, state SD2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: D.176, V.177, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, R.227, N.322, I.354, H.358, G.382, A.383, R.386 Chain B: D.317, R.343, R.346 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:T.223, A:L.224, A:G.382, A:R.386, B:R.343 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.346 ATP.2: 15 residues within 4Å: Chain C: M.150, G.152, G.193, T.194, G.195, K.196, T.197, L.198, D.249, A.294, I.328, H.332, A.357 Chain D: D.297, R.326 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:D.297, C:G.152, C:G.193, C:G.195, C:K.196, C:T.197, C:T.197, C:A.294 Salt bridges: D:R.326, C:K.196 ATP.3: 18 residues within 4Å: Chain D: D.166, I.167, G.168, M.170, P.207, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, T.347, I.348, G.372, A.373, N.376 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:T.213, D:M.214, D:D.265 Salt bridges: D:K.212 ATP.4: 22 residues within 4Å: Chain A: R.333, R.336 Chain F: D.187, I.188, G.189, L.191, G.227, P.228, P.229, G.230, T.231, G.232, K.233, T.234, L.235, D.286, T.332, N.333, I.365, H.369, G.393, K.397 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:G.227, F:P.229, F:G.232, F:K.233, F:T.234, F:L.235, F:N.333 Salt bridges: A:R.333, A:R.333, A:R.336

6 x LDZ: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide(Non-covalent)

LDZ.5: 14 residues within 4Å: Chain N: T.35, R.53, T.54, T.55, A.61, K.67, R.79, G.81, S.82, A.83, T.86, M.129 Chain O: Y.157, H.159 10 PLIP interactions: 8 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: N:T.54, N:A.61, N:K.67, N:T.86, O:Y.157 Hydrogen bonds: N:T.55, N:T.55, N:G.81, N:A.83 pi-Stacking: O:H.159 LDZ.6: 18 residues within 4Å: Chain O: T.44, R.62, A.63, T.64, E.65, G.66, A.70, K.76, G.88, G.90, T.91, A.92, T.95 Chain P: R.99, D.125, L.126, I.127, C.129 10 PLIP interactions: 7 interactions with chain O, 3 interactions with chain P Hydrophobic interactions: O:T.44, O:A.70, O:A.92, P:L.126, P:I.127, P:I.127 Hydrogen bonds: O:T.64, O:G.90, O:G.90, O:A.92 LDZ.7: 15 residues within 4Å: Chain R: T.60, R.78, A.79, T.80, A.86, V.90, K.92, M.104, A.105, G.106, A.108 Chain S: D.153, P.154, V.155, S.157 15 PLIP interactions: 10 interactions with chain R, 5 interactions with chain S Hydrophobic interactions: R:A.79, R:A.86, R:V.90, R:K.92, S:D.153, S:P.154, S:V.155, S:V.155 Hydrogen bonds: R:T.60, R:R.78, R:T.80, R:T.80, R:G.106, R:A.108, S:D.153 LDZ.9: 16 residues within 4Å: Chain d: T.35, R.53, T.54, T.55, T.56, A.61, T.65, R.79, G.81, S.82, A.83, D.85, T.86, M.129 Chain e: Y.157, H.159 12 PLIP interactions: 11 interactions with chain d, 1 interactions with chain e Hydrophobic interactions: d:T.54, d:A.61, d:T.65, d:A.83, e:Y.157 Hydrogen bonds: d:T.35, d:R.53, d:T.55, d:T.55, d:T.55, d:G.81, d:A.83 LDZ.10: 14 residues within 4Å: Chain e: T.44, A.63, T.64, E.65, A.70, C.74, K.76, G.88, G.90, T.91, A.92, T.95 Chain f: D.125, I.127 13 PLIP interactions: 11 interactions with chain e, 2 interactions with chain f Hydrophobic interactions: e:T.44, e:A.63, e:E.65, e:A.70, e:T.91, e:A.92 Hydrogen bonds: e:T.44, e:T.64, e:T.64, e:G.90, e:G.90, f:D.125, f:D.125 LDZ.11: 14 residues within 4Å: Chain h: T.60, R.78, A.79, T.80, A.81, A.86, V.90, K.92, M.104, A.105, G.106, G.107, A.108 Chain i: D.153 10 PLIP interactions: 9 interactions with chain h, 1 interactions with chain i Hydrophobic interactions: h:A.79, h:A.86, h:V.90 Hydrogen bonds: h:T.60, h:T.80, h:T.80, h:T.80, h:G.106, h:A.108, i:D.153

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain 2: W.111, H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:H.113, 2:H.115, 2:D.126, 2:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-11-02

Peptides

26S proteasome regulatory subunit 7: A
26S proteasome regulatory subunit 4: B
26S protease regulatory subunit 8: C
26S proteasome regulatory subunit 6B: D
26S protease regulatory subunit 10B: E
26S proteasome regulatory subunit 6A: F
Proteasome subunit alpha type-6: G6
Proteasome subunit alpha type-2: H7
Proteasome subunit alpha type-4: I8
Proteasome subunit alpha type-7: J9
Proteasome subunit alpha type-5: Ka
Proteasome subunit alpha type-1: Lb
Proteasome subunit alpha type-3: Mc
Proteasome subunit beta type-6: Nd
Proteasome subunit beta type-7: Oe
Proteasome subunit beta type-3: Pf
Proteasome subunit beta type-2: Qg
Proteasome subunit beta type-5: Rh
Proteasome subunit beta type-1: Si
Proteasome subunit beta type-4: Tj
26S proteasome non-ATPase regulatory subunit 1: U
26S proteasome non-ATPase regulatory subunit 3: V
26S proteasome non-ATPase regulatory subunit 12: W
26S proteasome non-ATPase regulatory subunit 11: X
26S proteasome non-ATPase regulatory subunit 6: Y
26S proteasome non-ATPase regulatory subunit 7: Z
26S proteasome non-ATPase regulatory subunit 13: 0
26S proteasome non-ATPase regulatory subunit 4: 1
26S proteasome non-ATPase regulatory subunit 14: 2
26S proteasome non-ATPase regulatory subunit 8: 3
26S proteasome complex subunit SEM1: 4
26S proteasome non-ATPase regulatory subunit 2: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

6
g

H
H

7
h

I
I

8
i

J
J

9
j

K
K

a
k

L
L

b
l

M
M

c
m

N
N

d
n

O
O

e
o

P
P

f
p

Q
Q

g
q

R
R

h
r

S
S

i
s

T
T

j
t

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S protease regulatory subunit 8

26S proteasome regulatory subunit 6B

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

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

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

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