SMTL ID : 8ro2.1

Integrative Structure of the human intron lariat Spliceosome (ILS'')

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE

GTP.1: 19 residues within 4Å: Chain C: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, G.178, V.179, G.180, G.207, H.208, K.259, D.261, R.262, S.311, S.312, Q.313 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:H.139, C:G.141, C:K.142, C:T.143, C:T.143, C:T.143, C:C.144, C:D.164, C:G.178, C:G.180, C:G.207, C:H.208, C:K.259, C:E.266, C:S.312, C:Q.313, C:Q.313 Salt bridges: C:H.139, C:K.142, C:K.142, C:D.261

3 x ZN: ZINC ION

ZN.2: 5 residues within 4Å: Chain J: C.105, C.117, C.119, C.134 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.105, J:C.117, J:C.119, J:C.134 ZN.3: 5 residues within 4Å: Chain J: C.101, C.102, C.105, C.137 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.101, J:C.102, J:C.105, J:C.137 ZN.4: 4 residues within 4Å: Chain J: C.101, C.119, C.139, C.142 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.101, J:C.119, J:C.139, J:C.142

1 x IHP: INOSITOL HEXAKISPHOSPHATE

IHP.5: 11 residues within 4Å: Chain 0: R.163, K.442, H.584, K.606, K.609, H.610, Y.613, Y.614, N.617, K.623, G.624 13 PLIP interactions: 13 interactions with chain 0 Hydrogen bonds: 0:N.617 Salt bridges: 0:R.163, 0:K.442, 0:K.442, 0:H.584, 0:K.606, 0:K.606, 0:K.609, 0:K.609, 0:K.609, 0:H.610, 0:K.623, 0:K.623

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vorlander, M.K. et al., Mechanism for the initiation of spliceosome disassembly. Nature (2024)

Release Date

2024-09-18

Peptides

116 kDa U5 small nuclear ribonucleoprotein component: C
Pre-mRNA-splicing factor ISY1 homolog: D
ATP-dependent RNA helicase DHX15: E
U5 small nuclear ribonucleoprotein 40 kDa protein: F
Crooked neck-like protein 1: G
Pre-mRNA-splicing factor SPF27: H
CWF19-like protein 1: I
Protein BUD31 homolog: J
Pre-mRNA-splicing factor RBM22: K
Intron-binding protein aquarius: L
SNW domain-containing protein 1: M
Peptidyl-prolyl cis-trans isomerase-like 1: N
Pre-mRNA-processing factor 17: O
Coiled-coil domain-containing protein 12: P
Small nuclear ribonucleoprotein Sm D3: Q
Small nuclear ribonucleoprotein Sm D1: R
Small nuclear ribonucleoprotein Sm D2: S
Small nuclear ribonucleoprotein E: T
Small nuclear ribonucleoprotein F: U
Small nuclear ribonucleoprotein G: V
Pre-mRNA-processing factor 19: Wbcd
Splicing regulator SDE2: X
Splicing factor ESS-2 homolog: Y
Pre-mRNA-processing-splicing factor 8: 0
Pre-mRNA-splicing factor SYF1: 1
Cell division cycle 5-like protein: 3
CWF19-like protein 2: 4
Pre-mRNA-splicing factor SYF2: 5
Spliceosome-associated protein CWC15 homolog: 6
PAX3- and PAX7-binding protein 1: 7
Pleiotropic regulator 1: 8
Tuftelin-interacting protein 11: 9
Small nuclear ribonucleoprotein-associated proteins B and B': a

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
C

D
D

E
DX

F
E

G
J

H
K

I
L1

J
N

K
O

L
Q

M
R

N
S

O
W

P
Z

Q
a

R
c

S
d

T
e

U
f

V
g

W
s

b
q

c
r

d
t

X
z

Y
3

0
A

1
I

3
L

4
L2

5
M

6
P

7
PX

8
T

9
TF

a
b

116 kDa U5 small nuclear ribonucleoprotein component

Pre-mRNA-splicing factor ISY1 homolog

ATP-dependent RNA helicase DHX15

U5 small nuclear ribonucleoprotein 40 kDa protein

Crooked neck-like protein 1

Pre-mRNA-splicing factor SPF27

CWF19-like protein 1

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Intron-binding protein aquarius

SNW domain-containing protein 1

Peptidyl-prolyl cis-trans isomerase-like 1

Pre-mRNA-processing factor 17

Coiled-coil domain-containing protein 12

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Pre-mRNA-processing factor 19

Splicing regulator SDE2

Splicing factor ESS-2 homolog

Pre-mRNA-processing-splicing factor 8

Pre-mRNA-splicing factor SYF1

Cell division cycle 5-like protein

CWF19-like protein 2

Pre-mRNA-splicing factor SYF2

Spliceosome-associated protein CWC15 homolog

PAX3- and PAX7-binding protein 1

Pleiotropic regulator 1

Tuftelin-interacting protein 11

Small nuclear ribonucleoprotein-associated proteins B and B'

Related Entries With Identical Sequence