SMTL ID : 9dtr.1

Structure of the yeast post-catalytic P complex spliceosome at 2.3 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 6 residues within 4Å: Chain C: A.59, G.60, U.80 Chain G: A.21 Chain J: G.95 Ligands: K.2 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain E: T.147, D.179, S.190 Ligands: GTP.6 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.147, E:S.190

4 x K: POTASSIUM ION(Non-functional Binders)

K.2: 5 residues within 4Å: Chain C: G.52, A.59, G.60, U.80 Ligands: MG.1 No protein-ligand interaction detected (PLIP) K.3: 4 residues within 4Å: Chain C: C.61, G.78, U.80, G.81 No protein-ligand interaction detected (PLIP) K.4: 5 residues within 4Å: Chain C: G.50, A.51 Chain J: G.1, U.2, G.95 No protein-ligand interaction detected (PLIP) K.8: 5 residues within 4Å: Chain C: G.60, G.78, U.80 Chain G: G.20, A.21 No protein-ligand interaction detected (PLIP)

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)(Covalent)

IHP.5: 12 residues within 4Å: Chain 0: K.171 Chain D: R.236, K.517, Y.655, H.659, K.684, H.685, Y.688, Y.689, N.692, K.697, G.698 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain 0 Hydrogen bonds: D:Y.688, D:Y.689, D:G.698 Salt bridges: D:K.228, D:R.236, D:K.517, D:K.517, D:K.517, D:H.659, D:H.659, D:K.684, D:K.684, D:K.684, D:H.685, 0:K.171 IHP.15: 10 residues within 4Å: Chain S: K.356, Y.365, T.402, F.403, S.404, K.405, K.436, A.437, K.438, K.441 14 PLIP interactions: 13 interactions with chain S, 1 interactions with chain X Hydrogen bonds: S:Y.365, S:S.404, S:S.404, S:K.405, S:A.437, S:K.438 Salt bridges: S:K.356, S:K.356, S:K.405, S:K.405, S:K.436, S:K.438, S:K.441, X:K.102

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

GTP.6: 21 residues within 4Å: Chain E: P.141, L.142, H.143, S.144, G.145, K.146, T.147, S.148, L.189, S.190, A.215, P.216, G.217, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.7 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:H.143, E:G.145, E:K.146, E:T.147, E:S.148, E:S.190, E:S.190, E:G.217, E:H.218, E:N.268, E:K.269, E:K.269, E:T.316, E:T.316, E:K.317 Salt bridges: E:H.143, E:K.146, E:K.146, E:D.271 pi-Cation interactions: E:K.269

7 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain M: C.104, C.105, C.108, C.148 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.104, M:C.105, M:C.108, M:C.148 ZN.10: 5 residues within 4Å: Chain M: C.104, C.122, C.150, C.153 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.104, M:C.122, M:C.150, M:C.153 ZN.11: 6 residues within 4Å: Chain M: C.108, C.120, C.122, C.145 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.108, M:C.120, M:C.122, M:C.145 ZN.12: 4 residues within 4Å: Chain N: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.73, N:C.81, N:C.87, N:H.91 ZN.13: 4 residues within 4Å: Chain O: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.34, O:C.37, O:C.61, O:C.64 ZN.14: 4 residues within 4Å: Chain O: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.13, O:C.16, O:C.71, O:C.74 ZN.16: 4 residues within 4Å: Chain 0: C.122, C.125, H.130, C.135 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.122, 0:C.125, 0:H.130, 0:C.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senn, K.A. et al., Control of 3' splice site selection by the yeast splicing factor Fyv6. eLife (2024)

Release Date

2024-12-25

Peptides

Pre-mRNA-splicing factor 8: D
Pre-mRNA-splicing factor SNU114: E
Protein FYV6: F
Pre-mRNA-splicing factor ISY1: H
Pre-mRNA-splicing factor CWC22: I
Pre-mRNA-splicing factor PRP46: K
Pre-mRNA-processing protein 45: L
Pre-mRNA-splicing factor BUD31: M
Pre-mRNA-splicing factor CWC2: N
Pre-mRNA-splicing factor SLT11: O
Pre-mRNA-splicing factor CEF1: P
Pre-mRNA-splicing factor CWC15: Q
Pre-mRNA-splicing factor CWC21: R
Pre-mRNA-splicing factor CLF1: S
Pre-mRNA-splicing factor SYF1: T
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22: U
U2 small nuclear ribonucleoprotein A': V
U2 small nuclear ribonucleoprotein B'': W
Pre-mRNA-splicing factor NTC20: X
Pre-mRNA-splicing factor 18: Y
Small nuclear ribonucleoprotein-associated protein B: Z7
Pre-mRNA-splicing factor SLU7: 0
Small nuclear ribonucleoprotein Sm D3: 1a
Small nuclear ribonucleoprotein E: 2c
Small nuclear ribonucleoprotein F: 3d
Small nuclear ribonucleoprotein G: 4e
Small nuclear ribonucleoprotein Sm D1: 58
Small nuclear ribonucleoprotein Sm D2: 69
Pre-mRNA-processing factor 17: b
Pre-mRNA-splicing factor SNT309: f
Pre-mRNA-processing factor 19: ghij
Pre-mRNA-splicing factor SYF2: k

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
C

F
D

H
G

I
H

K
J

L
K

M
L

N
M

O
N

P
O

Q
P

R
R

S
S

T
T

U
V

V
W

W
Y

X
Z

Y
a

Z
b

7
k

0
c

1
d

a
n

2
e

c
p

3
f

d
q

4
g

e
r

5
h

8
l

6
j

9
m

b
o

f
s

g
t

h
u

i
v

j
w

k
y

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing factor SNU114

Protein FYV6

Pre-mRNA-splicing factor ISY1

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'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor NTC20

Pre-mRNA-splicing factor 18

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 17

Pre-mRNA-splicing factor SNT309

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SYF2

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