SMTL ID : 8hk1.1

The cryo-EM structure of human pre-17S U2 snRNP

Coordinates

PDB Format Compare

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-mer

Ligands

1 x 9B0: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate(Non-covalent)

9B0.1: 13 residues within 4Å: Chain B: L.1066, K.1067, K.1071, R.1074, R.1075, V.1110, V.1114, E.1121, F.1153, Y.1157 Chain G: Y.36, V.37, R.38 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:V.1110, B:V.1114, B:V.1114, B:F.1153, B:F.1153, B:F.1153, B:Y.1157, G:V.37 Hydrogen bonds: B:L.1066, G:R.38 Salt bridges: B:R.1074, B:E.1121 pi-Cation interactions: B:Y.1157

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain G: C.23, K.25, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.23, G:C.26, G:C.58, G:C.61 ZN.3: 5 residues within 4Å: Chain G: C.11, C.46, E.48, C.49, C.85 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.11, G:C.46, G:C.49, G:C.85 ZN.4: 4 residues within 4Å: Chain G: C.30, C.33, C.72, C.75 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.30, G:C.33, G:C.72, G:C.75 ZN.5: 4 residues within 4Å: Chain J: C.408, C.411, H.425, H.431 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.408, J:H.425, J:H.431

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, F. et al., Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Nat Commun (2023)

Release Date

2023-03-08

Peptides

Splicing factor 3B subunit 1: B
Splicing factor 3B subunit 2: C
Splicing factor 3B subunit 3: D
Splicing factor 3B subunit 4: E
Splicing factor 3B subunit 5: F
PHD finger-like domain-containing protein 5A: G
Splicing factor 3A subunit 1: H
Splicing factor 3A subunit 2: I
Splicing factor 3A subunit 3: J
HIV Tat-specific factor 1: K
ATP-dependent RNA helicase DDX42: L
U2 small nuclear ribonucleoprotein A': M
U2 small nuclear ribonucleoprotein B'': N
Small nuclear ribonucleoprotein Sm D2: O
Small nuclear ribonucleoprotein F: P
Small nuclear ribonucleoprotein E: Q
Small nuclear ribonucleoprotein G: R
Small nuclear ribonucleoprotein Sm D3: S
Small nuclear ribonucleoprotein-associated proteins B and B': T
Small nuclear ribonucleoprotein Sm D1: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
1

C
2

D
3

E
4

F
5

G
6

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
a

P
b

Q
c

R
d

S
e

T
f

U
g

Splicing factor 3B subunit 1

Splicing factor 3B subunit 2

Splicing factor 3B subunit 3

Splicing factor 3B subunit 4

Splicing factor 3B subunit 5

PHD finger-like domain-containing protein 5A

Splicing factor 3A subunit 1

Splicing factor 3A subunit 2

Splicing factor 3A subunit 3

HIV Tat-specific factor 1

ATP-dependent RNA helicase DDX42

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D1

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