SMTL ID : 5ylz.1

Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Covalent)

IHP.1: 8 residues within 4Å: Chain A: R.236, K.517, H.659, K.684, H.685, Y.688, K.697, G.698 12 PLIP interactions: 12 interactions with chain A Salt bridges: A:R.236, A:K.517, A:K.517, A:K.517, A:H.659, A:H.659, A:K.684, A:K.684, A:K.684, A:H.685, A:K.697, A:K.697

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

GTP.2: 20 residues within 4Å: Chain A: P.406 Chain C: L.142, H.143, S.144, G.145, K.146, T.147, S.148, L.189, S.190, G.217, H.218, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:H.143, C:S.144, C:G.145, C:K.146, C:T.147, C:T.147, C:S.148, C:S.190, C:G.217, C:K.269, C:K.317 Salt bridges: C:H.143, C:K.146, C:K.146, C:D.271

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

MG.3: 4 residues within 4Å: Chain C: T.147, S.190, D.214 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.147, C:S.190 MG.4: 5 residues within 4Å: Chain D: G.60, G.78, U.80 Chain E: G.13, U.365 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain D: A.59, G.60, U.80 Chain E: G.364, U.365 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain D: U.80, G.81 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain D: G.81 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain L: C.104, C.105, C.108, C.148 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.104, L:C.105, L:C.108, L:C.148 ZN.10: 4 residues within 4Å: Chain L: C.104, C.122, C.150, C.153 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.104, L:C.122, L:C.150, L:C.153 ZN.11: 5 residues within 4Å: Chain L: C.108, C.120, C.122, C.145 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.108, L:C.120, L:C.122, L:C.145 ZN.12: 5 residues within 4Å: Chain N: C.13, C.16, C.71, C.73, C.74 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.13, N:C.71, N:C.73, N:C.74 ZN.13: 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.14: 5 residues within 4Å: Chain O: C.73, C.81, C.87, Y.89, H.91 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.73, O:C.81, O:C.87, O:H.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, R. et al., Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae. Cell (2017)

Release Date

2018-07-18

Peptides

Pre-mRNA-splicing factor 8: A
Pre-mRNA-splicing factor SNU114: C
Pre-mRNA-splicing factor SNT309: G
Pre-mRNA-splicing factor SYF1: H
Pre-mRNA-splicing factor CLF1: I
Pre-mRNA-splicing factor CEF1: J
Pre-mRNA-splicing factor SYF2: K
Pre-mRNA-splicing factor BUD31: L
Pre-mRNA-processing factor 17: M
Pre-mRNA-splicing factor SLT11: N
Pre-mRNA-splicing factor CWC2: O
Pre-mRNA-splicing factor PRP46: P
Pre-mRNA-splicing factor CWC15: Q
Pre-mRNA-processing protein 45: R
Pre-mRNA-splicing factor CWC21: S
Pre-mRNA-splicing factor CWC22: T
Pre-mRNA-splicing factor 18: U
Pre-mRNA-splicing factor SLU7: V
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22: W
Small nuclear ribonucleoprotein-associated protein B: X4
Small nuclear ribonucleoprotein E: Y5
Small nuclear ribonucleoprotein F: Z6
Small nuclear ribonucleoprotein G: 07
Small nuclear ribonucleoprotein Sm D3: 18
Small nuclear ribonucleoprotein Sm D1: 29
Small nuclear ribonucleoprotein Sm D2: 3a
U2 small nuclear ribonucleoprotein A': b
U2 small nuclear ribonucleoprotein B'': c
Pre-mRNA-processing factor 19: defg

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
G

H
H

I
I

J
J

K
K

L
L

M
T

N
M

O
N

P
O

Q
P

R
Q

S
R

T
S

U
U

V
V

W
W

X
a

4
h

Y
b

5
i

Z
c

6
j

0
d

7
k

1
e

8
l

2
f

9
m

3
g

a
n

b
o

c
p

d
q

e
r

f
s

g
t

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor SNT309

Pre-mRNA-splicing factor SYF1

Pre-mRNA-splicing factor CLF1

Pre-mRNA-splicing factor CEF1

Pre-mRNA-splicing factor SYF2

Pre-mRNA-splicing factor BUD31

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor SLT11

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor PRP46

Pre-mRNA-splicing factor CWC15

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor CWC22

Pre-mRNA-splicing factor 18

Pre-mRNA-splicing factor SLU7

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

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 A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-processing factor 19

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