SMTL ID : 5lj3.1

Structure of the core of the yeast spliceosome immediately after branching

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-2-2-2-1-1-1-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 G: C.51, C.54, C.88, C.91 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:C.51, G:C.54, G:C.88, G:C.91, G:C.91 ZN.5: 6 residues within 4Å: Chain N: C.104, C.105, C.108, C.148 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.104, N:C.105, N:C.108, N:C.148 ZN.6: 7 residues within 4Å: Chain N: C.104, C.108, C.122, C.150, C.153 Ligands: ZN.5, ZN.7 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.104, N:C.122, N:C.150, N:C.153 ZN.7: 7 residues within 4Å: Chain N: C.108, C.120, C.122, C.145, C.150 Ligands: ZN.5, ZN.6 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:C.108, N:C.120, N:C.122, N:C.145, N:C.150 ZN.8: 5 residues within 4Å: Chain E: A.35 Chain O: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.73, O:C.81, O:C.87, O:H.91 ZN.9: 6 residues within 4Å: Chain P: C.34, C.37, C.61, R.63, C.64, S.114 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.34, P:C.37, P:C.61 ZN.10: 4 residues within 4Å: Chain P: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.13, P:C.16, P:C.71, P:C.74

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

GTP.4: 21 residues within 4Å: Chain I: 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 I Hydrogen bonds: I:H.143, I:G.145, I:K.146, I:T.147, I:T.147, I:S.148, I:S.190, I:A.215, I:G.217, I:H.218, I:K.269, I:T.316, I:T.316, I:K.317 Salt bridges: I:H.143, I:H.143, I:H.143, I:K.146, I:K.146 pi-Cation interactions: I: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

2016-08-03

Peptides

Pre-mRNA-splicing factor 8: F
Protein CWC16: G
Pre-mRNA-splicing factor CWC25: H
Pre-mRNA-splicing factor SNU114: I
ISY1: J
CWC22: K
PRP46: L
Pre-mRNA-processing protein 45: M
Pre-mRNA-splicing factor BUD31: N
CWC2: O
Pre-mRNA-splicing factor SLT11: P
CEF1: Q
CWC15: R
Pre-mRNA-splicing factor CWC21: S
CLF1: T
SYF1: U
Small nuclear ribonucleoprotein-associated protein B: V4
Small nuclear ribonucleoprotein Sm D3: W7
Small nuclear ribonucleoprotein E: X8
Small nuclear ribonucleoprotein F: Y9
Small nuclear ribonucleoprotein G: Za
Small nuclear ribonucleoprotein Sm D1: 05
Small nuclear ribonucleoprotein Sm D2: 16
U2 small nuclear ribonucleoprotein A': 2
U2 small nuclear ribonucleoprotein B'': 3
unknown: b

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

F
A

G
D

H
F

I
C

J
G

K
H

L
J

M
K

N
L

O
M

P
N

Q
O

R
P

S
R

T
S

U
T

V
b

4
k

W
d

7
n

X
e

8
p

Y
f

9
q

Z
g

a
r

0
h

5
l

1
j

6
m

2
W

3
Y

b
x

Pre-mRNA-splicing factor 8

Protein CWC16

Pre-mRNA-splicing factor CWC25

Pre-mRNA-splicing factor SNU114

ISY1

CWC22

PRP46

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor BUD31

CWC2

Pre-mRNA-splicing factor SLT11

CEF1

CWC15

Pre-mRNA-splicing factor CWC21

CLF1

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''

unknown

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