SMTL ID : 6exn.1

Post-catalytic P complex spliceosome with 3' splice site docked

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-2-2-2-2-2-2-1-1-4-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 6 residues within 4Å: Chain C: A.59, G.60, A.79, U.80 Chain G: A.21 Chain I: G.95 No protein-ligand interaction detected (PLIP)

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 13 residues within 4Å: Chain D: R.236, K.517, H.659, K.681, K.684, H.685, Y.688, Y.689, K.697, G.698 Chain Z: W.167, R.170, K.171 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain Z Hydrogen bonds: D:Y.689, D:G.698 Salt bridges: D:R.236, D:K.517, D:K.517, D:H.659, D:H.659, D:K.681, D:K.681, D:K.684, D:K.684, D:K.684, D:H.685, D:K.697, Z:R.170, Z:K.171

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 23 residues within 4Å: Chain D: P.406 Chain E: P.141, L.142, H.143, S.144, G.145, K.146, T.147, S.148, P.174, R.176, L.189, S.190, P.216, G.217, H.218, K.269, D.271, R.272, D.276, S.315, T.316, K.317 22 PLIP interactions: 22 interactions with chain E Hydrogen bonds: E:H.143, E:S.144, E:G.145, E:G.145, E:K.146, E:T.147, E:T.147, E:S.148, E:S.190, E:G.217, E:H.218, E:K.269, E:T.316, E:T.316, E:K.317, E:K.317 Salt bridges: E:H.143, E:K.146, E:K.146, E:D.271, E:D.276 pi-Cation interactions: E:K.269

7 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain L: C.104, C.105, C.108, C.148 Ligands: ZN.5, ZN.6 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.104, L:C.105, L:C.108, L:C.148 ZN.5: 6 residues within 4Å: Chain L: C.104, C.122, C.150, C.153 Ligands: ZN.4, ZN.6 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.104, L:C.122, L:C.150, L:C.153 ZN.6: 7 residues within 4Å: Chain L: C.108, C.120, C.122, C.145, H.147 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.108, L:C.120, L:C.122, L:C.145 ZN.7: 4 residues within 4Å: Chain M: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.73, M:C.81, M:C.87, M:H.91 ZN.8: 4 residues within 4Å: Chain N: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.34, N:C.37, N:C.61, N:C.64 ZN.9: 4 residues within 4Å: Chain N: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.13, N:C.16, N:C.71, N:C.74 ZN.10: 4 residues within 4Å: Chain Z: C.122, C.125, H.130, C.135 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.122, Z:C.125, Z:H.130, Z:C.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkinson, M.E. et al., Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection. Science (2017)

Release Date

2018-01-17

Peptides

Pre-mRNA-splicing factor Prp8: D
Pre-mRNA-splicing factor SNU114: E
Pre-mRNA-splicing factor CWC16: F
Pre-mRNA-splicing factor CWC22: H
Pre-mRNA-splicing factor PRP46: J
Pre-mRNA-processing protein 45: K
Pre-mRNA-splicing factor BUD31: L
Pre-mRNA-splicing factor CWC2: M
Pre-mRNA-splicing factor SLT11: N
Pre-mRNA-splicing factor CEF1: O
Pre-mRNA-splicing factor CWC15: P
Pre-mRNA-splicing factor CWC21: Q
Pre-mRNA-splicing factor CLF1: R
Pre-mRNA-splicing factor SYF1: S
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22: T
U2 small nuclear ribonucleoprotein A': U
Unassigned structure: V
U2 small nuclear ribonucleoprotein B'': W
Pre-mRNA-splicing factor Prp18: X
Small nuclear ribonucleoprotein-associated protein B: Y6
Pre-mRNA-splicing factor SLU7: Z
Small nuclear ribonucleoprotein Sm D3: 09
Small nuclear ribonucleoprotein E: 1b
Small nuclear ribonucleoprotein F: 2c
Small nuclear ribonucleoprotein G: 3d
Small nuclear ribonucleoprotein Sm D1: 47
Small nuclear ribonucleoprotein Sm D2: 58
Pre-mRNA-processing factor Prp17: a
Pre-mRNA-splicing factor SNT309: e
Pre-mRNA-processing factor Prp19: fghi
Pre-mRNA-splicing factor SYF2: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
C

F
D

H
H

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
R

R
S

S
T

T
V

U
W

V
X

W
Y

X
a

Y
b

6
k

Z
c

0
d

9
n

1
e

b
p

2
f

c
q

3
g

d
r

4
h

7
l

5
j

8
m

a
o

e
s

f
t

g
u

h
v

i
w

j
y

Pre-mRNA-splicing factor Prp8

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor CWC16

Pre-mRNA-splicing factor CWC22

Pre-mRNA-splicing factor PRP46

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor BUD31

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor SLT11

Pre-mRNA-splicing factor CEF1

Pre-mRNA-splicing factor CWC15

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor CLF1

Pre-mRNA-splicing factor SYF1

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22

U2 small nuclear ribonucleoprotein A'

Unassigned structure

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor Prp18

Small nuclear ribonucleoprotein-associated protein B

Pre-mRNA-splicing factor SLU7

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Pre-mRNA-processing factor Prp17

Pre-mRNA-splicing factor SNT309

Pre-mRNA-processing factor Prp19

Pre-mRNA-splicing factor SYF2

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