SMTL ID : 5wsg.1

Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.00 Å

Oligo State

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

Ligands

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

GTP.1: 19 residues within 4Å: Chain A: P.406 Chain B: L.142, H.143, G.145, K.146, T.147, S.148, R.176, L.189, S.190, G.217, H.218, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.143, B:S.144, B:G.145, B:K.146, B:T.147, B:S.148, B:G.217, B:R.272, B:K.317 Salt bridges: B:H.143, B:H.143, B:K.146, B:K.146, B:D.271

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

MG.2: 4 residues within 4Å: Chain B: T.147, S.190, D.214 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.147, B:S.190 MG.9: 4 residues within 4Å: Chain K: G.13 Chain N: G.78, U.80 Chain g: U.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain N: A.59, A.79, U.80 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain N: G.81 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain N: G.81 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain N: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain F: C.13, C.16, C.71, C.73, C.74 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.13, F:C.71, F:C.73, F:C.74 ZN.4: 4 residues within 4Å: Chain F: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.34, F:C.37, F:C.61, F:C.64 ZN.5: 5 residues within 4Å: Chain G: C.73, C.81, C.87, H.91 Chain N: A.35 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.73, G:C.81, G:C.87, G:H.91 ZN.6: 5 residues within 4Å: Chain I: C.104, C.105, C.108, C.148 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.104, I:C.105, I:C.108, I:C.148 ZN.7: 4 residues within 4Å: Chain I: C.104, C.122, C.150, C.153 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.104, I:C.122, I:C.150, I:C.153 ZN.8: 5 residues within 4Å: Chain I: C.108, C.120, C.122, C.145 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.108, I:C.120, I:C.122, I:C.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, C. et al., Structure of a yeast step II catalytically activated spliceosome. Science (2017)

Release Date

2017-01-25

Peptides

Pre-mRNA-splicing factor 8: A
Pre-mRNA-splicing factor SNU114: B
Pre-mRNA-splicing factor CWC21: C
Pre-mRNA-splicing factor PRP46: D
Pre-mRNA-processing protein 45: E
Pre-mRNA-splicing factor SLT11: F
Pre-mRNA-splicing factor CWC2: G
Pre-mRNA-splicing factor CWC15: H
Pre-mRNA-splicing factor BUD31: I
Pre-mRNA-splicing factor CWC22: J
Pre-mRNA-splicing factor CEF1,Pre-mRNA-splicing factor CEF1,Cef1,Pre-mRNA-splicing factor CEF1: Q
Pre-mRNA-splicing factor CLF1,Pre-mRNA-splicing factor CLF1,Clf1: R
Pre-mRNA-splicing factor SYF2: S
Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1: T
Pre-mRNA-processing factor 17: U
Pre-mRNA-processing factor 19: VWXY
Pre-mRNA-splicing factor SNT309: Z
Small nuclear ribonucleoprotein-associated protein B: 07
Small nuclear ribonucleoprotein E: 18
Small nuclear ribonucleoprotein F: 29
Small nuclear ribonucleoprotein G: 3a
Small nuclear ribonucleoprotein Sm D3: 4b
Small nuclear ribonucleoprotein Sm D1: 5c
Small nuclear ribonucleoprotein Sm D2: 6d
U2 small nuclear ribonucleoprotein B'': e
U2 small nuclear ribonucleoprotein A': f
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16: h
Pre-mRNA-splicing factor 18: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
J

D
O

E
P

F
Q

G
R

H
S

I
T

J
Z

Q
c

R
d

S
I

T
v

U
n

V
o

W
p

X
q

Y
r

Z
t

0
k

7
F

1
i

8
G

2
h

9
H

3
j

a
K

4
l

b
U

5
m

c
V

6
g

d
W

e
X

f
Y

h
e

i
f

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor PRP46

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor SLT11

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor CWC15

Pre-mRNA-splicing factor BUD31

Pre-mRNA-splicing factor CWC22

Pre-mRNA-splicing factor CEF1,Pre-mRNA-splicing factor CEF1,Cef1,Pre-mRNA-splicing factor CEF1

Pre-mRNA-splicing factor CLF1,Pre-mRNA-splicing factor CLF1,Clf1

Pre-mRNA-splicing factor SYF2

Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1

Pre-mRNA-processing factor 17

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SNT309

Small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

U2 small nuclear ribonucleoprotein B''

U2 small nuclear ribonucleoprotein A'

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

Pre-mRNA-splicing factor 18

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