SMTL ID : 5y88.1

Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.46 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 U- U- U- U- U- U- U- U- U: RNA (intron or U6 snRNA)(Non-covalent)

U-U-U-U-U-U-U-U-U.1: 15 residues within 4Å: Chain W: N.180, R.198, E.313, G.346, S.347, K.398, P.521, S.550, V.551, N.618, I.619, P.683, T.702, S.703, K.704 Protein-ligand interaction information (PLIP) not available

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 11 residues within 4Å: Chain A: R.236, K.517, H.659, K.681, K.684, H.685, Y.688, N.692, K.697, G.698, Y.1620 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.692 Salt bridges: A:R.236, A:K.517, A:K.517, A:K.517, A:H.659, A:H.659, A:K.681, A:K.684, A:K.684, A:K.684, A:H.685, A:K.697, A:K.697, A:K.697

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

GTP.3: 18 residues within 4Å: Chain C: L.142, H.143, G.145, K.146, T.147, S.148, R.176, L.189, S.190, G.217, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:H.143, C:G.145, C:K.146, C:T.147, C:S.148, C:S.148, C:S.190, C:S.190, C:G.217, C:K.269, C:S.315, C:T.316, 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.4: 3 residues within 4Å: Chain C: T.147, S.190 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.147, C:S.190 MG.5: 2 residues within 4Å: Chain D: G.78, U.80 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain D: A.59, A.79, U.80 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain D: G.77, G.81 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain D: G.81 No protein-ligand interaction detected (PLIP) MG.9: 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.10: 6 residues within 4Å: Chain L: C.104, C.105, C.108, C.148 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.104, L:C.105, L:C.108, L:C.148 ZN.11: 5 residues within 4Å: Chain L: C.104, C.122, C.150, C.153 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.104, L:C.122, L:C.150, L:C.153 ZN.12: 6 residues within 4Å: Chain L: C.108, C.120, C.122, C.145, C.148 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.108, L:C.120, L:C.122, L:C.145 ZN.13: 5 residues within 4Å: Chain M: C.13, C.16, C.71, C.73, C.74 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.13, M:C.71, M:C.73, M:C.74 ZN.14: 4 residues within 4Å: Chain M: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.34, M:C.37, M:C.61, M:C.64 ZN.15: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, R. et al., Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae. Cell(Cambridge,Mass.) (2017)

Release Date

2018-08-01

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-splicing factor SLT11: M
Pre-mRNA-splicing factor CWC2: N
Pre-mRNA-splicing factor PRP46: O
Pre-mRNA-splicing factor CWC15: P
Pre-mRNA-processing protein 45: Q
Protein CWC16: R
Pre-mRNA-processing factor 17: S
Pre-mRNA-splicing factor CWC23: T
Pre-mRNA-splicing factor SPP382: U
Pre-mRNA-splicing factor NTR2: V
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43: W
Small nuclear ribonucleoprotein-associated protein B: X6
Small nuclear ribonucleoprotein E: Y7
Small nuclear ribonucleoprotein F: Z8
Small nuclear ribonucleoprotein G: 09
Small nuclear ribonucleoprotein Sm D3: 1a
Small nuclear ribonucleoprotein Sm D1: 2b
Small nuclear ribonucleoprotein Sm D2: 3c
U2 small nuclear ribonucleoprotein A': 4
U2 small nuclear ribonucleoprotein B'': 5
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
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
a

6
h

Y
b

7
i

Z
c

8
j

0
d

9
k

1
e

a
l

2
f

b
m

3
g

c
n

4
o

5
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-splicing factor SLT11

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor PRP46

Pre-mRNA-splicing factor CWC15

Pre-mRNA-processing protein 45

Protein CWC16

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor CWC23

Pre-mRNA-splicing factor SPP382

Pre-mRNA-splicing factor NTR2

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43

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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