SMTL ID : 5lj5.1

Overall structure of the yeast spliceosome immediately after branching.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

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

Ligands

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

MG.1: 4 residues within 4Å: Chain B: G.16 Chain E: G.60, G.77, G.78 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain C: G.1 Chain E: G.60, U.80 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain H: C.51, C.54, C.88, C.91 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.51, H:C.54, H:C.88, H:C.91, H:C.91 ZN.5: 6 residues within 4Å: Chain O: C.104, C.105, C.108, C.148 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.104, O:C.105, O:C.108, O:C.148 ZN.6: 7 residues within 4Å: Chain O: C.104, C.108, C.122, C.150, C.153 Ligands: ZN.5, ZN.7 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.104, O:C.122, O:C.150, O:C.153 ZN.7: 7 residues within 4Å: Chain O: C.108, C.120, C.122, C.145, C.150 Ligands: ZN.5, ZN.6 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:C.108, O:C.120, O:C.122, O:C.145, O:C.150 ZN.8: 5 residues within 4Å: Chain E: A.35 Chain P: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.73, P:C.81, P:C.87, P:H.91 ZN.9: 6 residues within 4Å: Chain Q: C.34, C.37, C.61, R.63, C.64, S.114 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.34, Q:C.37, Q:C.61, Q:C.64 ZN.10: 4 residues within 4Å: Chain Q: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.13, Q:C.16, Q:C.71, Q:C.74

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

GTP.4: 21 residues within 4Å: Chain J: L.142, H.143, G.145, K.146, T.147, S.148, P.174, R.176, G.188, L.189, S.190, A.215, G.217, H.218, N.268, K.269, D.271, R.272, S.315, T.316, K.317 20 PLIP interactions: 20 interactions with chain J Hydrogen bonds: J:H.143, J:G.145, J:K.146, J:T.147, J:T.147, J:S.148, J:S.190, J:A.215, J:G.217, J:H.218, J:K.269, J:T.316, J:T.316, J:K.317 Salt bridges: J:H.143, J:H.143, J:H.143, J:K.146, J:K.146 pi-Cation interactions: J:K.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galej, W.P. et al., Cryo-EM structure of the spliceosome immediately after branching. Nature (2016)

Release Date

2016-08-31

Peptides

Pre-mRNA-splicing factor 8: F
Pre-mRNA-splicing helicase BRR2: G
Protein CWC16: H
Pre-mRNA-splicing factor CWC25: I
Pre-mRNA-splicing factor SNU114: J
Pre-mRNA-splicing factor ISY1: K
CWC22: L
Pre-mRNA-splicing factor PRP46: M
Pre-mRNA-processing protein 45: N
Pre-mRNA-splicing factor BUD31: O
Pre-mRNA-splicing factor CWC2: P
Pre-mRNA-splicing factor SLT11: Q
Pre-mRNA-splicing factor CEF1: R
CWC15: S
Pre-mRNA-splicing factor CWC21: T
Pre-mRNA-splicing factor CLF1: U
Pre-mRNA-splicing factor SYF1: V
Small nuclear ribonucleoprotein-associated protein B: W5
Small nuclear ribonucleoprotein Sm D3: X8
Small nuclear ribonucleoprotein E: Y9
Small nuclear ribonucleoprotein F: Za
Small nuclear ribonucleoprotein G: 0b
Small nuclear ribonucleoprotein Sm D1: 16
Small nuclear ribonucleoprotein Sm D2: 27
U2 small nuclear ribonucleoprotein A': 3
U2 small nuclear ribonucleoprotein B'': 4
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16: c
Pre-mRNA-processing factor 19: defg
Pre-mRNA-splicing factor SNT309: h
unknown: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

F
A

G
B

H
D

I
F

J
C

K
G

L
H

M
J

N
K

O
L

P
M

Q
N

R
O

S
P

T
R

U
S

V
T

W
b

5
k

X
d

8
n

Y
e

9
p

Z
f

a
q

0
g

b
r

1
h

6
l

2
j

7
m

3
W

4
Y

c
Q

d
t

e
u

f
v

g
w

h
s

i
x

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing helicase BRR2

Protein CWC16

Pre-mRNA-splicing factor CWC25

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor ISY1

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

CWC15

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor CLF1

Pre-mRNA-splicing factor SYF1

Small nuclear ribonucleoprotein-associated protein B

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

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

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

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SNT309

unknown

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