SMTL ID : 3jcm.1

Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 18 residues within 4Å: Chain A: P.406 Chain H: L.142, H.143, S.144, G.145, K.146, T.147, S.148, R.176, L.189, S.190, G.217, K.269, D.271, R.272, S.315, T.316, K.317 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:H.143, H:S.144, H:G.145, H:T.147, H:T.147, H:T.147, H:S.148, H:S.190, 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:R.176, H:D.271

1 x M7M: N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)(Non-covalent)

M7M.2: 7 residues within 4Å: Chain 5: U.80, G.81, A.82 Chain 6: A.1 Chain E: E.362, L.363, F.391 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, R. et al., The 3.8 angstrom structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis. Science (2016)

Release Date

2016-02-24

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
Pre-mRNA-splicing helicase BRR2: I
Small nuclear ribonucleoprotein Sm D3: JQ
Small nuclear ribonucleoprotein-associated protein B: KR
Small nuclear ribonucleoprotein Sm D1: LS
Small nuclear ribonucleoprotein Sm D2: MT
Small nuclear ribonucleoprotein E: NU
Small nuclear ribonucleoprotein F: OV
Small nuclear ribonucleoprotein G: PW
U6 snRNA-associated Sm-like protein LSm8: X
U6 snRNA-associated Sm-like protein LSm2: Y
U6 snRNA-associated Sm-like protein LSm3: Z
U6 snRNA-associated Sm-like protein LSm6: 0
U6 snRNA-associated Sm-like protein LSm5: 1
U6 snRNA-associated Sm-like protein LSm7: 2
U6 snRNA-associated Sm-like protein LSm4: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
I

D
G

E
K

F
L

G
M

H
H

I
N

J
R

Q
J

K
S

R
O

L
T

S
P

M
U

T
Q

N
V

U
Y

O
W

V
Z

P
X

W
a

X
b

Y
c

Z
d

0
e

1
f

2
g

3
h

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

Pre-mRNA-splicing helicase BRR2

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

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

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