SMTL ID : 6tm5.1

Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

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

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain B: C.23, M.28, H.56 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.23, B:M.28, B:H.56 ZN.2: 4 residues within 4Å: Chain B: C.51, H.53, C.73, C.76 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.51, B:H.53, B:C.76 ZN.3: 6 residues within 4Å: Chain B: C.33, C.34, D.36, C.37, K.38, C.44 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alfieri, C. et al., A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase. Embo Rep. (2020)

Release Date

2020-02-19

Peptides

Anaphase-promoting complex subunit 1: A
Anaphase-promoting complex subunit 11: B
Cell division cycle protein 23 homolog: CP
Anaphase-promoting complex subunit 15: D
Anaphase-promoting complex subunit 16: E
Cell division cycle protein 27 homolog: FH
Anaphase-promoting complex subunit CDC26: GR
Anaphase-promoting complex subunit 4: I
Cell division cycle protein 16 homolog: JK
Anaphase-promoting complex subunit 10: L
Anaphase-promoting complex subunit 13: M
Anaphase-promoting complex subunit 2: N
Anaphase-promoting complex subunit 5: O
Apc1 loop: Q
Anaphase-promoting complex subunit 7: ST
Serine/threonine-protein kinase Nek2: U
Serine/threonine-protein kinase Nek2: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

P
P

D
D

E
E

F
F

H
H

G
G

R
W

I
I

J
J

K
K

L
L

M
M

N
N

O
O

Q
T

S
X

T
Y

U
S

V
Q

Anaphase-promoting complex subunit 1

Anaphase-promoting complex subunit 11

Cell division cycle protein 23 homolog

Anaphase-promoting complex subunit 15

Anaphase-promoting complex subunit 16

Cell division cycle protein 27 homolog

Anaphase-promoting complex subunit CDC26

Anaphase-promoting complex subunit 4

Cell division cycle protein 16 homolog

Anaphase-promoting complex subunit 10

Anaphase-promoting complex subunit 13

Anaphase-promoting complex subunit 2

Anaphase-promoting complex subunit 5

Apc1 loop

Anaphase-promoting complex subunit 7

Serine/threonine-protein kinase Nek2

Serine/threonine-protein kinase Nek2

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