SMTL ID : 5nrl.1

Structure of a pre-catalytic spliceosome.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-3-3-3-3-3-3-3-1-1-1-mer

Ligands

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

GTP.1: 18 residues within 4Å: Chain J: L.142, H.143, S.144, G.145, K.146, T.147, S.148, P.174, R.176, L.189, S.190, P.216, G.217, K.269, R.272, S.315, T.316, K.317 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:H.143, J:S.144, J:G.145, J:K.146, J:T.147, J:T.147, J:S.148, J:S.190, J:S.190, J:S.190, J:G.217, J:K.269, J:R.272, J:T.316, J:K.317 Salt bridges: J:H.143, J:K.146, J:K.146

7 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain S: C.82, C.85, H.98, H.104 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.82, S:C.85, S:H.98, S:H.104 ZN.3: 4 residues within 4Å: Chain Z: C.11, C.46, C.49, C.86 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.11, Z:C.46, Z:C.49, Z:C.86 ZN.4: 4 residues within 4Å: Chain Z: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.23, Z:C.26, Z:C.58, Z:C.61 ZN.5: 4 residues within 4Å: Chain Z: C.30, C.33, C.73, C.76 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.30, Z:C.33, Z:C.73, Z:C.76 ZN.6: 4 residues within 4Å: Chain 0: C.282, C.285, H.298, H.304 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.282, 0:C.285, 0:H.298, 0:H.304 ZN.7: 5 residues within 4Å: Chain 0: C.423, I.425, C.426, H.440, H.446 5 PLIP interactions: 5 interactions with chain 0 Metal complexes: 0:C.423, 0:C.426, 0:H.440, 0:H.440, 0:H.446 ZN.8: 4 residues within 4Å: Chain 1: C.68, C.71, H.84, H.90 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.68, 1:C.71, 1:H.84, 1:H.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plaschka, C. et al., Structure of a pre-catalytic spliceosome. Nature (2017)

Release Date

2017-05-31

Peptides

U6 snRNA-associated Sm-like protein LSm3: B
U6 snRNA-associated Sm-like protein LSm7: F
U6 snRNA-associated Sm-like protein LSm8: G
Pre-mRNA-splicing factor 8: H
Pre-mRNA-splicing helicase BRR2: I
Pre-mRNA-splicing factor SNU114: J
Spliceosomal protein DIB1: K
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component: L
Pre-mRNA-processing factor 31: M
U4/U6 small nuclear ribonucleoprotein PRP3: N
U4/U6 small nuclear ribonucleoprotein PRP4: O
Pre-mRNA-splicing factor 6: Q
13 kDa ribonucleoprotein-associated protein: R
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component: S
Pre-mRNA-splicing factor 38: T
Pre-mRNA-splicing factor SPP381: U
U2 snRNP component HSH155: V
Pre-mRNA-splicing factor RSE1: W
Cold sensitive U2 snRNA suppressor 1: X
Protein HSH49: Y
Pre-mRNA-splicing factor RDS3: Z
Pre-mRNA-splicing factor PRP9: 0
Pre-mRNA-splicing factor PRP11: 1
Pre-mRNA-splicing factor PRP21: 2
U2 small nuclear ribonucleoprotein A': 3
Unknown: 4
U2 small nuclear ribonucleoprotein B'': 5
RDS3 complex subunit 10: 6
U6 snRNA-associated Sm-like protein LSm2: 7
Small nuclear ribonucleoprotein-associated protein B: 8go
Small nuclear ribonucleoprotein Sm D3: 9jr
Small nuclear ribonucleoprotein E: als
Small nuclear ribonucleoprotein F: bmt
Small nuclear ribonucleoprotein G: cnu
Small nuclear ribonucleoprotein Sm D1: dhp
Small nuclear ribonucleoprotein Sm D2: eiq
U6 snRNA-associated Sm-like protein LSm4: f
U6 snRNA-associated Sm-like protein LSm5: k
U6 snRNA-associated Sm-like protein LSm6: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
3

F
7

G
8

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
H

Q
J

R
K

S
L

T
M

U
N

V
O

W
P

X
Q

Y
R

Z
S

0
T

1
U

2
V

3
W

4
X

5
Y

6
Z

7
a

8
b

g
k

o
s

9
d

j
n

r
v

a
e

l
p

s
w

b
f

m
q

t
x

c
g

n
r

u
y

d
h

h
l

p
t

e
i

i
m

q
u

f
j

k
o

v
z

U6 snRNA-associated Sm-like protein LSm3

U6 snRNA-associated Sm-like protein LSm7

U6 snRNA-associated Sm-like protein LSm8

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing helicase BRR2

Pre-mRNA-splicing factor SNU114

Spliceosomal protein DIB1

66 kDa U4/U6.U5 small nuclear ribonucleoprotein component

Pre-mRNA-processing factor 31

U4/U6 small nuclear ribonucleoprotein PRP3

U4/U6 small nuclear ribonucleoprotein PRP4

Pre-mRNA-splicing factor 6

13 kDa ribonucleoprotein-associated protein

23 kDa U4/U6.U5 small nuclear ribonucleoprotein component

Pre-mRNA-splicing factor 38

Pre-mRNA-splicing factor SPP381

U2 snRNP component HSH155

Pre-mRNA-splicing factor RSE1

Cold sensitive U2 snRNA suppressor 1

Protein HSH49

Pre-mRNA-splicing factor RDS3

Pre-mRNA-splicing factor PRP9

Pre-mRNA-splicing factor PRP11

Pre-mRNA-splicing factor PRP21

U2 small nuclear ribonucleoprotein A'

Unknown

U2 small nuclear ribonucleoprotein B''

RDS3 complex subunit 10

U6 snRNA-associated Sm-like protein LSm2

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

U6 snRNA-associated Sm-like protein LSm4

U6 snRNA-associated Sm-like protein LSm5

U6 snRNA-associated Sm-like protein LSm6

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