SMTL ID : 3jb9.1

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x G- U- A- U- G- U- A- U: RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')(Non-covalent)

G-U-A-U-G-U-A-U.1: 18 residues within 4Å: Chain A: T.554, T.555, K.556, K.559 Chain N: G.32, A.33, U.34, A.35, C.36, A.37, G.38, A.39, A.67 Chain O: A.9, A.10 Chain U: R.191 Chain X: K.364, K.366 Protein-ligand interaction information (PLIP) not available

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 14 residues within 4Å: Chain B: H.151, H.152, G.153, K.154, S.155, A.156, S.192, N.270, K.271, D.273, R.274, S.323, C.324, D.325 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.151, B:G.153, B:K.154, B:S.155, B:S.155, B:A.156, B:S.192, B:N.270, B:K.271, B:C.324, B:D.325 Salt bridges: B:K.154, B:D.273, B:D.325

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

MG.3: 3 residues within 4Å: Chain N: G.48, G.66, U.68 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain N: G.40, A.47, G.48, A.67, U.68 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain N: G.65, G.66, U.68, G.69 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain N: U.51, G.69 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain V: C.117, C.125, C.131, H.135 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.117, V:C.125, V:C.131, V:H.135 ZN.8: 4 residues within 4Å: Chain W: C.44, C.47, C.70, C.73 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:C.44, W:C.70 ZN.9: 5 residues within 4Å: Chain W: C.23, C.26, C.80, S.82, C.83 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.23, W:C.26, W:C.80, W:C.83 ZN.10: 5 residues within 4Å: Chain X: C.412, L.414, C.415, H.455, H.502 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:C.412, X:C.415, X:H.502 ZN.11: 6 residues within 4Å: Chain Z: C.101, C.102, C.105, C.137, C.139 Ligands: ZN.12 5 PLIP interactions: 5 interactions with chain Z Metal complexes: Z:C.101, Z:C.102, Z:C.105, Z:C.137, Z:C.139 ZN.12: 7 residues within 4Å: Chain Z: C.101, C.105, C.119, C.139, C.142 Ligands: ZN.11, ZN.13 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.101, Z:C.119, Z:C.139, Z:C.142 ZN.13: 6 residues within 4Å: Chain Z: C.105, C.117, C.119, C.134, C.139 Ligands: ZN.12 5 PLIP interactions: 5 interactions with chain Z Metal complexes: Z:C.105, Z:C.117, Z:C.119, Z:C.134, Z:C.139

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.14: 11 residues within 4Å: Chain 5: Y.725, T.726, R.751, C.752, G.753, K.754, H.755, V.756, Y.1046, T.1066, R.1177 7 PLIP interactions: 7 interactions with chain 5 Hydrogen bonds: 5:T.726, 5:R.751, 5:C.752, 5:G.753, 5:K.754 Salt bridges: 5:H.755 pi-Stacking: 5:Y.725

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, C. et al., Structure of a yeast spliceosome at 3.6-angstrom resolution. Science (2015)

Release Date

2015-09-23

Peptides

Pre-mRNA-splicing factor spp42: A
Pre-mRNA-splicing factor cwf10: B
Small nuclear ribonucleoprotein Sm D3: D8
Small nuclear ribonucleoprotein-associated protein B: E9
Small nuclear ribonucleoprotein Sm D1: Fa
Small nuclear ribonucleoprotein Sm D2: Gb
Small nuclear ribonucleoprotein E: Hc
Small nuclear ribonucleoprotein F: Id
Small nuclear ribonucleoprotein G: Je
Pre-mRNA-splicing factor prp5: K
Pre-mRNA-splicing factor cwf17: L
Pre-mRNA-processing protein 45: M
Pre-mRNA-processing factor 19: QRST
Pre-mRNA-splicing factor cdc5: U
Pre-mRNA-splicing factor cwf2: V
Pre-mRNA-splicing factor cwf5: W
Pre-mRNA-splicing factor cwf19: X
Peptidyl-prolyl cis-trans isomerase ppi1: Y
Pre-mRNA-splicing factor cwf14: Z
Pre-mRNA-processing factor 17: 0
Pre-mRNA-splicing factor cwf15: 1
Pre-mRNA-splicing factor cwf7: 2
Pre-mRNA-splicing factor cwf4: 3
Pre-mRNA-splicing factor cwf3: 4
Pre-mRNA-splicing factor cwf11: 5
U2 small nuclear ribonucleoprotein A': 6
Probable U2 small nuclear ribonucleoprotein B'': 7
unknown chain: f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

8
Z

E
E

9
b

F
F

a
f

G
G

b
l

H
H

c
m

I
I

d
n

J
J

e
o

K
K

L
L

M
M

Q
S

R
T

S
U

T
V

U
W

V
Y

W
a

X
c

Y
d

Z
e

0
g

1
h

2
i

3
R

4
r

5
X

6
j

7
k

f
x

Pre-mRNA-splicing factor spp42

Pre-mRNA-splicing factor cwf10

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Pre-mRNA-splicing factor prp5

Pre-mRNA-splicing factor cwf17

Pre-mRNA-processing protein 45

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor cdc5

Pre-mRNA-splicing factor cwf2

Pre-mRNA-splicing factor cwf5

Pre-mRNA-splicing factor cwf19

Peptidyl-prolyl cis-trans isomerase ppi1

Pre-mRNA-splicing factor cwf14

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor cwf15

Pre-mRNA-splicing factor cwf7

Pre-mRNA-splicing factor cwf4

Pre-mRNA-splicing factor cwf3

Pre-mRNA-splicing factor cwf11

U2 small nuclear ribonucleoprotein A'

Probable U2 small nuclear ribonucleoprotein B''

unknown chain