SMTL ID : 5zwm.1

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.40 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-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, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:H.143, H:S.144, H:G.145, H:K.146, H:T.147, H:S.148, H:S.148, H:S.190, H:S.190, H:G.217, H:N.268, H:T.316, H:K.317 Salt bridges: H:H.143, H:H.143, H:K.146, H:K.146, H:D.271

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain H: T.147, S.190 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.147, H:S.190

6 x ZN: ZINC ION(Non-covalent)

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

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: S
Small nuclear ribonucleoprotein Sm D3: T4e
Small nuclear ribonucleoprotein-associated protein B: U1a
Small nuclear ribonucleoprotein Sm D1: V2f
Small nuclear ribonucleoprotein Sm D2: W3g
Small nuclear ribonucleoprotein E: X5b
Small nuclear ribonucleoprotein F: Y6c
Small nuclear ribonucleoprotein G: Z7d
Pre-mRNA-splicing helicase BRR2: 0
U2 small nuclear ribonucleoprotein A': h
U2 small nuclear ribonucleoprotein B'': i
U2 snRNP component HSH155: j
Cold sensitive U2 snRNA suppressor 1: k
Pre-mRNA-splicing factor RSE1: l
Protein HSH49: m
Pre-mRNA-splicing factor RDS3: n
RDS3 complex subunit 10: o
U2 snRNP component IST3: p
Pre-mRNA-splicing factor CWC26: q
Pre-mRNA leakage protein 1: r
Pre-mRNA-splicing factor PRP9: s
Pre-mRNA-splicing factor PRP21: t
Pre-mRNA-splicing factor PRP11: u

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

S
O

T
d

4
S

e
l

U
a

1
P

a
h

V
b

2
Q

f
m

W
c

3
R

g
n

X
e

5
T

b
i

Y
f

6
U

c
j

Z
g

7
V

d
k

0
D

h
o

i
p

j
1

k
2

l
3

m
4

n
5

o
6

p
X

q
Y

r
Z

s
u

t
w

u
v

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 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

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

Pre-mRNA-splicing factor PRP9

Pre-mRNA-splicing factor PRP21

Pre-mRNA-splicing factor PRP11

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