SMTL ID : 6qw6.1

Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 14 residues within 4Å: Chain R: R.139, K.418, Y.556, H.560, K.582, K.585, H.586, Y.589, Y.590, N.593, K.599, G.600, P.601 Chain X: E.275 16 PLIP interactions: 16 interactions with chain R Hydrogen bonds: R:Y.590, R:N.593, R:G.600 Salt bridges: R:K.131, R:R.139, R:K.418, R:K.418, R:K.418, R:H.560, R:H.560, R:K.582, R:K.585, R:K.585, R:K.585, R:H.586, R:K.599

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain T: T.40, D.66, D.101, T.102 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.40

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

GTP.3: 24 residues within 4Å: Chain R: P.311 Chain T: L.35, H.36, H.37, G.38, K.39, T.40, C.41, D.61, G.75, V.76, G.77, P.103, G.104, H.105, N.155, K.156, D.158, R.159, E.163, S.208, S.209, Q.210 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain T Hydrogen bonds: T:H.36, T:H.37, T:G.38, T:G.38, T:K.39, T:T.40, T:C.41, T:D.61, T:G.77, T:G.104, T:H.105, T:K.156, T:K.156, T:E.163, T:S.209, T:Q.210 Salt bridges: T:H.36, T:H.36, T:K.39, T:K.39, T:D.158 pi-Cation interactions: T:K.156

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain c: C.136, C.139, H.155, H.161 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.136, c:C.139, c:H.155, c:H.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Charenton, C. et al., Mechanism of 5' splice site transfer for human spliceosome activation. Science (2019)

Release Date

2019-04-17

Peptides

U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein: A
Small nuclear ribonucleoprotein Sm D1: CO
Small nuclear ribonucleoprotein Sm D2: DP
Small nuclear ribonucleoprotein Sm D3: EQ
U4/U6 small nuclear ribonucleoprotein Prp3: F
U4/U6 small nuclear ribonucleoprotein Prp4: G
U4/U6 small nuclear ribonucleoprotein Prp31: H
NHP2-like protein 1: I
Small nuclear ribonucleoprotein-associated proteins B and B': JY
Small nuclear ribonucleoprotein E: KZ
Small nuclear ribonucleoprotein F: L0
Small nuclear ribonucleoprotein G: M1
Pre-mRNA-processing-splicing factor 8: R
U5 small nuclear ribonucleoprotein 200 kDa helicase: S
116 kDa U5 small nuclear ribonucleoprotein component: T
Thioredoxin-like protein 4A: U
Pre-mRNA-processing factor 6: V
U5 small nuclear ribonucleoprotein 40 kDa protein: W
Probable ATP-dependent RNA helicase DDX23: X
U6 snRNA-associated Sm-like protein LSm2: 3
U6 snRNA-associated Sm-like protein LSm3: 4
U6 snRNA-associated Sm-like protein LSm4: 5
U6 snRNA-associated Sm-like protein LSm5: 6
U6 snRNA-associated Sm-like protein LSm6: 7
U6 snRNA-associated Sm-like protein LSm7: 8
U6 snRNA-associated Sm-like protein LSm8: 9
RNA-binding protein 42: a
U4/U6.U5 tri-snRNP-associated protein 1: b
U4/U6.U5 tri-snRNP-associated protein 2: c

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

C
41

O
51

D
42

P
52

E
43

Q
53

F
4A

G
4B

H
4C

I
4D

J
4b

Y
5b

K
4e

Z
5e

L
4f

0
5f

M
4g

1
5g

R
5A

S
5B

T
5C

U
5D

V
5J

W
5O

X
5X

3
62

4
63

5
64

6
65

7
66

8
67

9
68

a
R

b
S

c
U

U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein Sm D3

U4/U6 small nuclear ribonucleoprotein Prp3

U4/U6 small nuclear ribonucleoprotein Prp4

U4/U6 small nuclear ribonucleoprotein Prp31

NHP2-like protein 1

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Pre-mRNA-processing-splicing factor 8

U5 small nuclear ribonucleoprotein 200 kDa helicase

116 kDa U5 small nuclear ribonucleoprotein component

Thioredoxin-like protein 4A

Pre-mRNA-processing factor 6

U5 small nuclear ribonucleoprotein 40 kDa protein

Probable ATP-dependent RNA helicase DDX23

U6 snRNA-associated Sm-like protein LSm2

U6 snRNA-associated Sm-like protein LSm3

U6 snRNA-associated Sm-like protein LSm4

U6 snRNA-associated Sm-like protein LSm5

U6 snRNA-associated Sm-like protein LSm6

U6 snRNA-associated Sm-like protein LSm7

U6 snRNA-associated Sm-like protein LSm8

RNA-binding protein 42

U4/U6.U5 tri-snRNP-associated protein 1

U4/U6.U5 tri-snRNP-associated protein 2

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