SMTL ID : 6fvw.1

26S proteasome, s4 state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 22 residues within 4Å: Ligands: MG.2 Chain f: D.169, G.171, P.211, G.212, T.213, G.214, K.215, T.216, L.217, R.220, E.269, N.315, I.347, H.351, G.375, A.376, R.379 Chain g: D.262, R.288, P.289, R.291 21 PLIP interactions: 7 interactions with chain g, 14 interactions with chain f Water bridges: g:N.259, g:R.291, g:R.291, f:T.216 Salt bridges: g:R.288, g:R.288, g:R.288, g:R.291, f:K.215, f:K.215 Hydrogen bonds: f:G.171, f:G.212, f:T.213, f:T.213, f:G.214, f:K.215, f:T.216, f:T.216, f:L.217, f:R.220, f:E.269 ATP.3: 20 residues within 4Å: Ligands: MG.4 Chain g: G.133, G.174, T.175, G.176, K.177, T.178, L.179, D.230, E.231, T.276, I.309, H.313, G.337, A.338, Q.341 Chain k: N.275, D.278, R.304, R.307 20 PLIP interactions: 9 interactions with chain k, 11 interactions with chain g Hydrogen bonds: k:N.275, k:D.278, g:G.133, g:G.133, g:G.174, g:T.175, g:G.176, g:T.178, g:E.231, g:E.231, g:Q.341 Water bridges: k:R.307, k:R.307 Salt bridges: k:R.304, k:R.304, k:R.307, k:R.307, k:R.307, g:K.177, g:K.177 ATP.9: 19 residues within 4Å: Ligands: MG.10 Chain f: R.326, R.329 Chain j: V.170, G.171, P.211, G.212, T.213, G.214, K.215, T.216, L.217, E.269, N.315, I.347, H.351, G.375, A.376, K.379 19 PLIP interactions: 13 interactions with chain j, 6 interactions with chain f Hydrogen bonds: j:G.171, j:G.212, j:T.213, j:T.213, j:G.214, j:K.215, j:T.216, j:N.315, j:N.315, f:R.329 Water bridges: j:D.268, j:D.268, f:R.326, f:R.326 Salt bridges: j:K.215, j:K.215, f:R.326, f:R.326, f:R.326 ATP.11: 20 residues within 4Å: Ligands: MG.12 Chain h: R.163, L.256, R.286, P.287, R.289 Chain k: M.147, G.190, T.191, G.192, K.193, T.194, L.195, R.198, I.248, I.325, H.329, G.353, A.354, K.357 19 PLIP interactions: 9 interactions with chain k, 10 interactions with chain h Hydrogen bonds: k:G.190, k:T.191, k:G.192, k:K.193, k:T.194, k:T.194, k:R.198, h:R.163, h:R.286 Salt bridges: k:K.193, k:K.193, h:R.286, h:R.286, h:R.286, h:R.289, h:R.289, h:R.289 Water bridges: h:R.289, h:R.289

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Ligands: ATP.1 Chain f: T.216 4 PLIP interactions: 1 interactions with chain f, 3 Ligand-Water interactions Metal complexes: f:T.216, H2O.1, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Ligands: ATP.3 Chain g: T.178 4 PLIP interactions: 1 interactions with chain g, 3 Ligand-Water interactions Metal complexes: g:T.178, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Ligands: ADP.5 Chain h: T.176, N.275 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Ligands: ADP.7 Chain i: T.181 5 PLIP interactions: 1 interactions with chain i, 4 Ligand-Water interactions Metal complexes: i:T.181, H2O.1, H2O.1, H2O.1, H2O.1 MG.10: 2 residues within 4Å: Ligands: ATP.9 Chain j: T.216 4 PLIP interactions: 1 interactions with chain j, 3 Ligand-Water interactions Metal complexes: j:T.216, H2O.1, H2O.1, H2O.1 MG.12: 2 residues within 4Å: Ligands: ATP.11 Chain k: T.194 4 PLIP interactions: 1 interactions with chain k, 3 Ligand-Water interactions Metal complexes: k:T.194, H2O.1, H2O.1, H2O.1

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

ADP.5: 16 residues within 4Å: Ligands: MG.6 Chain h: G.131, G.132, P.170, P.171, G.172, T.173, G.174, K.175, T.176, M.177, N.275, I.308, G.336, A.337, A.340 14 PLIP interactions: 14 interactions with chain h Hydrogen bonds: h:G.131, h:G.132, h:G.132, h:P.170, h:G.172, h:T.173, h:G.174, h:K.175, h:T.176, h:T.176, h:T.176, h:M.177, h:N.275 Salt bridges: h:K.175 ADP.7: 14 residues within 4Å: Ligands: MG.8 Chain i: I.135, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316, G.340, A.341 7 PLIP interactions: 7 interactions with chain i Hydrogen bonds: i:G.177, i:T.178, i:G.179, i:T.181, i:T.181, i:L.182 Salt bridges: i:K.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eisele, M.R. et al., Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Cell Rep (2018)

Release Date

2018-08-29

Peptides

Proteasome subunit alpha type-1: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-3: CQ
Proteasome subunit alpha type-4: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-6: FT
Probable proteasome subunit alpha type-7: GU
Proteasome subunit beta type-1: HV
Proteasome subunit beta type-2: IW
Proteasome subunit beta type-3: JX
Proteasome subunit beta type-4: KY
Proteasome subunit beta type-5: LZ
Proteasome subunit beta type-6: M0
Proteasome subunit beta type-7: N1
26S proteasome regulatory subunit RPN10: 2
Ubiquitin carboxyl-terminal hydrolase RPN11: 3
26S proteasome regulatory subunit RPN12: 4
26S proteasome regulatory subunit RPN13: 5
26S proteasome complex subunit SEM1: 6
26S proteasome regulatory subunit RPN1: 7
26S proteasome regulatory subunit RPN2: 8
26S proteasome regulatory subunit RPN3: 9
26S proteasome regulatory subunit RPN5: a
26S proteasome regulatory subunit RPN6: b
26S proteasome regulatory subunit RPN7: c
26S proteasome regulatory subunit RPN8: d
26S proteasome regulatory subunit RPN9: e
26S proteasome regulatory subunit 7 homolog: f
26S proteasome regulatory subunit 4 homolog: g
26S proteasome regulatory subunit 6B homolog: h
26S proteasome subunit RPT4: i
26S proteasome regulatory subunit 6A: j
26S proteasome regulatory subunit 8 homolog: k

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

O
A

B
b

P
B

C
c

Q
C

D
d

R
D

E
e

S
E

F
f

T
F

G
g

U
G

H
h

V
1

I
i

W
2

J
j

X
3

K
k

Y
4

L
l

Z
5

M
m

0
6

N
n

1
7

2
W

3
V

4
T

5
X

6
Y

7
Z

8
N

9
S

a
P

b
Q

c
R

d
U

e
O

f
H

g
I

h
K

i
L

j
M

k
J

Proteasome subunit alpha type-1

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit beta type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

26S proteasome regulatory subunit RPN10

Ubiquitin carboxyl-terminal hydrolase RPN11

26S proteasome regulatory subunit RPN12

26S proteasome regulatory subunit RPN13

26S proteasome complex subunit SEM1

26S proteasome regulatory subunit RPN1

26S proteasome regulatory subunit RPN2

26S proteasome regulatory subunit RPN3

26S proteasome regulatory subunit RPN5

26S proteasome regulatory subunit RPN6

26S proteasome regulatory subunit RPN7

26S proteasome regulatory subunit RPN8

26S proteasome regulatory subunit RPN9

26S proteasome regulatory subunit 7 homolog

26S proteasome regulatory subunit 4 homolog

26S proteasome regulatory subunit 6B homolog

26S proteasome subunit RPT4

26S proteasome regulatory subunit 6A

26S proteasome regulatory subunit 8 homolog

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