SMTL ID : 5l4g.1

The human 26S proteasome at 3.9 A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

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

Ligands

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

ATP.1: 23 residues within 4Å: Chain 2: D.176, V.177, G.178, G.179, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, N.322, I.354, I.357, H.358, G.382, A.383, R.386 Chain 3: D.317, R.343, R.346 Ligands: MG.2 16 PLIP interactions: 12 interactions with chain 2, 4 interactions with chain 3 Hydrogen bonds: 2:G.178, 2:G.178, 2:G.219, 2:T.220, 2:G.221, 2:K.222, 2:T.223, 2:L.224, 2:N.322, 2:H.358 Salt bridges: 2:K.222, 2:K.222, 3:R.343, 3:R.343, 3:R.343, 3:R.346 ATP.3: 22 residues within 4Å: Chain 3: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, K.237, N.332, I.364, I.367, H.368, G.392, A.393, K.396 Chain 7: R.307, R.310 Ligands: MG.4 16 PLIP interactions: 4 interactions with chain 7, 12 interactions with chain 3 Salt bridges: 7:R.307, 7:R.307, 7:R.307, 7:R.310, 3:K.232, 3:K.232 Hydrogen bonds: 3:G.188, 3:G.188, 3:G.229, 3:G.231, 3:K.232, 3:T.233, 3:L.234, 3:N.332, 3:H.368, 3:G.392 ATP.5: 24 residues within 4Å: Chain 4: D.166, I.167, G.168, G.169, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, T.347, I.348, G.372, A.373, N.376 Chain 5: D.265, A.288, R.291, R.294 Ligands: MG.6 14 PLIP interactions: 8 interactions with chain 4, 6 interactions with chain 5 Hydrogen bonds: 4:G.168, 4:G.209, 4:G.211, 4:K.212, 4:T.213, 4:M.214, 5:D.265, 5:D.265 Salt bridges: 4:K.212, 4:K.212, 5:R.291, 5:R.291, 5:R.291, 5:R.294 ATP.7: 26 residues within 4Å: Chain 5: E.134, I.135, G.136, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, R.185, E.234, N.280, I.312, I.315, H.316, G.340, A.341, R.344 Chain 6: D.318, A.341, R.344, G.346, R.347 Ligands: MG.8 19 PLIP interactions: 15 interactions with chain 5, 4 interactions with chain 6 Hydrogen bonds: 5:G.136, 5:G.136, 5:G.177, 5:T.178, 5:G.179, 5:K.180, 5:T.181, 5:T.181, 5:L.182, 5:N.280, 5:H.316, 5:R.344, 5:R.344 Salt bridges: 5:K.180, 5:K.180, 6:R.344, 6:R.344, 6:R.344, 6:R.347 ATP.9: 25 residues within 4Å: Chain 2: D.307, A.330, R.333, R.336 Chain 6: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, R.238, E.287, N.333, I.365, I.368, H.369, G.393, A.394, K.397 Ligands: MG.10 19 PLIP interactions: 15 interactions with chain 6, 4 interactions with chain 2 Hydrogen bonds: 6:G.189, 6:G.230, 6:T.231, 6:T.231, 6:G.232, 6:K.233, 6:T.234, 6:L.235, 6:R.238, 6:R.238, 6:N.333, 6:H.369, 6:K.397 Salt bridges: 6:K.233, 6:K.233, 2:R.333, 2:R.333, 2:R.333, 2:R.336

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain 2: K.222, T.223, D.275, E.276 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.223 MG.4: 4 residues within 4Å: Chain 3: K.232, T.233, D.285 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.233 MG.6: 4 residues within 4Å: Chain 4: T.213, D.265 Chain 5: D.265 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:T.213 MG.8: 4 residues within 4Å: Chain 5: K.180, T.181, E.234 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:T.181 MG.10: 5 residues within 4Å: Chain 2: D.307, R.336 Chain 6: T.234, D.286 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:T.234

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

ADP.11: 18 residues within 4Å: Chain 7: M.150, I.151, G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, R.201, I.328, I.331, H.332, G.356, A.357, K.360 11 PLIP interactions: 11 interactions with chain 7 Hydrogen bonds: 7:G.152, 7:G.152, 7:G.193, 7:G.195, 7:K.196, 7:T.197, 7:T.197, 7:L.198, 7:H.332 Salt bridges: 7:K.196, 7:K.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schweitzer, A. et al., Structure of the human 26S proteasome at a resolution of 3.9 angstrom. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-09-07

Peptides

Proteasome subunit alpha type-6: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-4: CQ
Proteasome subunit alpha type-7: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-1: FT
Proteasome subunit alpha type-3: 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 protease regulatory subunit 7: 2
26S protease regulatory subunit 4: 3
26S protease regulatory subunit 6B: 4
26S protease regulatory subunit 10B: 5
26S protease regulatory subunit 6A: 6
26S protease regulatory subunit 8: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

O
A

B
O

P
B

C
P

Q
C

D
Q

R
D

E
R

S
E

F
S

T
F

G
T

U
G

H
U

V
1

I
V

W
2

J
W

X
3

K
X

Y
4

L
Y

Z
5

M
Z

0
6

N
8

1
7

2
H

3
I

4
K

5
L

6
M

7
J

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-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 protease regulatory subunit 7

26S protease regulatory subunit 4

26S protease regulatory subunit 6B

26S protease regulatory subunit 10B

26S protease regulatory subunit 6A

26S protease regulatory subunit 8

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