SMTL ID : 5zwo.1

Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

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

Ligands

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

GTP.1: 19 residues within 4Å: Chain A: P.406 Chain H: L.142, H.143, S.144, G.145, K.146, T.147, S.148, L.189, S.190, G.217, K.269, D.271, R.272, S.315, T.316, K.317, L.318 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:H.143, H:G.145, H:K.146, H:T.147, H:S.148, H:S.148, H:S.190, H:G.217, H:S.315, H:T.316, H:K.317, H:L.318 Salt bridges: H:H.143, H:K.146, H:K.146, H:D.271

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain H: K.146, T.147, S.190 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.147, H:S.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, R. et al., Structures of the fully assembledSaccharomyces cerevisiaespliceosome before activation. Science (2018)

Release Date

2018-08-29

Peptides

Pre-mRNA-splicing factor 8: A
U4/U6 small nuclear ribonucleoprotein PRP4: B
Pre-mRNA-processing factor 31: C
Pre-mRNA-splicing factor 6: D
U4/U6 small nuclear ribonucleoprotein PRP3: E
Spliceosomal protein DIB1: F
13 kDa ribonucleoprotein-associated protein: G
Pre-mRNA-splicing factor SNU114: H
U6 snRNA-associated Sm-like protein LSm8: I
U6 snRNA-associated Sm-like protein LSm2: J
U6 snRNA-associated Sm-like protein LSm3: K
U6 snRNA-associated Sm-like protein LSm6: L
U6 snRNA-associated Sm-like protein LSm5: M
U6 snRNA-associated Sm-like protein LSm7: N
U6 snRNA-associated Sm-like protein LSm4: O
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component: R
Small nuclear ribonucleoprotein Sm D3: S4n
Small nuclear ribonucleoprotein-associated protein B: T1j
Small nuclear ribonucleoprotein Sm D1: U2o
Small nuclear ribonucleoprotein Sm D2: V3p
Small nuclear ribonucleoprotein E: W5k
Small nuclear ribonucleoprotein F: X6l
Small nuclear ribonucleoprotein G: Y7m
Pre-mRNA-splicing helicase BRR2: 0
U2 snRNP component HSH155: 9
Cold sensitive U2 snRNA suppressor 1: a
Pre-mRNA-splicing factor RSE1: b
Protein HSH49: c
Pre-mRNA-splicing factor RDS3: d
RDS3 complex subunit 10: e
U2 snRNP component IST3: f
Pre-mRNA-splicing factor CWC26: g
Pre-mRNA leakage protein 1: h
U2 small nuclear ribonucleoprotein A': q
U2 small nuclear ribonucleoprotein B'': r
Pre-mRNA-splicing factor PRP9: s
Pre-mRNA-splicing factor PRP21: t
Pre-mRNA-splicing factor PRP11: u
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component: v
Pre-mRNA-splicing factor 38: w
Pre-mRNA-splicing factor SPP381: x

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

C
L

D
N

E
J

F
E

G
M

H
C

I
z

J
q

K
r

L
x

M
t

N
y

O
s

R
O

S
d

4
S

n
l

T
a

1
P

j
h

U
b

2
Q

o
m

V
c

3
R

p
n

W
e

5
T

k
i

X
f

6
U

l
j

Y
g

7
V

m
k

0
D

9
1

a
2

b
3

c
4

d
5

e
6

f
X

g
Y

h
Z

q
o

r
p

s
u

t
w

u
v

v
W

w
0

x
9

Pre-mRNA-splicing factor 8

U4/U6 small nuclear ribonucleoprotein PRP4

Pre-mRNA-processing factor 31

Pre-mRNA-splicing factor 6

U4/U6 small nuclear ribonucleoprotein PRP3

Spliceosomal protein DIB1

13 kDa ribonucleoprotein-associated protein

Pre-mRNA-splicing factor SNU114

U6 snRNA-associated Sm-like protein LSm8

U6 snRNA-associated Sm-like protein LSm2

U6 snRNA-associated Sm-like protein LSm3

U6 snRNA-associated Sm-like protein LSm6

U6 snRNA-associated Sm-like protein LSm5

U6 snRNA-associated Sm-like protein LSm7

U6 snRNA-associated Sm-like protein LSm4

66 kDa U4/U6.U5 small nuclear ribonucleoprotein component

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 helicase BRR2

U2 snRNP component HSH155

Cold sensitive U2 snRNA suppressor 1

Pre-mRNA-splicing factor RSE1

Protein HSH49

Pre-mRNA-splicing factor RDS3

RDS3 complex subunit 10

U2 snRNP component IST3

Pre-mRNA-splicing factor CWC26

Pre-mRNA leakage protein 1

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor PRP9

Pre-mRNA-splicing factor PRP21

Pre-mRNA-splicing factor PRP11

23 kDa U4/U6.U5 small nuclear ribonucleoprotein component

Pre-mRNA-splicing factor 38

Pre-mRNA-splicing factor SPP381

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