SMTL ID : 9l5r.1

Cryo-EM structure of the thermophile spliceosome (state ILS)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-4-1-1-1-1-1-1-1-1-1-1-2-2-2-2-2-2-2-1-1-1-1-1-1-1-mer

Ligands

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

M7M.1: 9 residues within 4Å: Chain A: A.1 Chain E: H.132, E.147, R.150, W.154, E.158, A.159, W.162 Chain m: X.10 6 PLIP interactions: 6 interactions with chain E Salt bridges: E:H.132, E:R.150 pi-Stacking: E:W.162, E:W.162, E:W.162 pi-Cation interactions: E:R.150

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain F: T.178, S.222, D.246 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.178, F:S.222

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

GTP.3: 20 residues within 4Å: Chain D: P.449 Chain F: H.172, L.173, H.174, H.175, G.176, K.177, T.178, A.179, Q.206, L.221, S.222, G.249, K.301, D.303, R.304, C.355, T.356, S.357 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:H.174, F:H.175, F:G.176, F:K.177, F:T.178, F:A.179, F:Q.206, F:Q.206, F:S.222, F:K.301, F:T.356, F:T.356, F:S.357, F:S.357 Salt bridges: F:H.174, F:K.177, F:K.177, F:D.303 pi-Cation interactions: F:K.301

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.4: 14 residues within 4Å: Chain I: K.131, K.137 Chain K: K.361, R.365, T.405, F.406, A.407, K.408, K.439, D.440, K.441, R.444 Chain L: K.328, R.335 20 PLIP interactions: 13 interactions with chain K, 4 interactions with chain I, 3 interactions with chain L Hydrogen bonds: K:A.407, K:D.440, K:K.441 Salt bridges: K:K.361, K:K.361, K:R.365, K:K.408, K:K.408, K:K.439, K:K.439, K:K.439, K:K.441, K:R.444, I:K.131, I:K.131, I:K.137, I:K.137, L:K.328, L:K.328, L:R.335

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain R: C.103, C.104, C.107, C.139 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.103, R:C.104, R:C.107, R:C.139 ZN.6: 5 residues within 4Å: Chain R: C.103, C.121, C.141, C.144 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.103, R:C.121, R:C.141, R:C.144 ZN.7: 6 residues within 4Å: Chain R: C.107, C.119, C.121, C.136 Ligands: ZN.5, ZN.6 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.107, R:C.119, R:C.121, R:C.136 ZN.8: 5 residues within 4Å: Chain U: C.512, L.514, C.515, H.562, H.609 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.512, U:C.515, U:H.562, U:H.609 ZN.9: 4 residues within 4Å: Chain V: C.44, C.47, C.72, C.75 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.44, V:C.47, V:C.72, V:C.75 ZN.10: 4 residues within 4Å: Chain V: C.23, C.26, C.82, C.85 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.23, V:C.26, V:C.82, V:C.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates. Cell Res. (2025)

Release Date

2025-03-12

Peptides

PRP8: D
Pre-mRNA-splicing factor SYF2: E
SNU114: F
SDE2: G
Anaphase-promoting complex subunit 4-like WD40 domain-containing protein: H
CCDC12: I
Putative pre-mRNA splicing protein: J
Suppressor of forked domain-containing protein: K
Putative pre-mRNA splicing protein: L
Pre-mRNA-splicing factor SPF27: M
Pre-mRNA-processing factor 19: NOPQ
Putative bud site selection protein: R
Peptidyl-prolyl cis-trans isomerase: S
Pre-mRNA-splicing factor PRP46: T
Cell cycle control protein: U
Putative pre-mRNA splicing protein: V
Putative pre-mRNA splicing protein: W
Pre-mRNA-processing protein 45: X
PRP17: Y
Putative pre-mRNA splicing protein: Z
Pre-mRNA-splicing factor: 0
Small nuclear ribonucleoprotein E: 1a
Sm protein F: 2c
Delta(14)-sterol reductase: 3d
Small nuclear ribonucleoprotein Sm D1: 4e
Sm protein B: 5f
Small nuclear ribonucleoprotein Sm D3: 6g
Small nuclear ribonucleoprotein G: 7b
U2 small nuclear ribonucleoprotein A': 8
U2 small nuclear ribonucleoprotein B'-like protein: 9
Nineteen complex-related protein 2-domain-containing protein: h
G-patch domain-containing protein: i
RNA helicase: j
Putative cyclophilin protein: l
Unknown protein: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
D

H
E

I
F

J
I

K
J

L
L

M
K

N
q

O
t

P
r

Q
s

R
N

S
S

T
T

U
U

V
M

W
0

X
R

Y
W

Z
P

0
Y

1
a

a
j

2
b

c
l

3
c

d
m

4
d

e
o

5
e

f
p

6
f

g
u

7
g

b
k

8
h

9
i

h
CY

i
Cb

j
Cc

l
Ci

m
H

PRP8

Pre-mRNA-splicing factor SYF2

SNU114

SDE2

Anaphase-promoting complex subunit 4-like WD40 domain-containing protein

CCDC12

Putative pre-mRNA splicing protein

Suppressor of forked domain-containing protein

Putative pre-mRNA splicing protein

Pre-mRNA-splicing factor SPF27

Pre-mRNA-processing factor 19

Putative bud site selection protein

Peptidyl-prolyl cis-trans isomerase

Pre-mRNA-splicing factor PRP46

Cell cycle control protein

Putative pre-mRNA splicing protein

Putative pre-mRNA splicing protein

Pre-mRNA-processing protein 45

PRP17

Putative pre-mRNA splicing protein

Pre-mRNA-splicing factor

Small nuclear ribonucleoprotein E

Sm protein F

Delta(14)-sterol reductase

Small nuclear ribonucleoprotein Sm D1

Sm protein B

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein G

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B'-like protein

Nineteen complex-related protein 2-domain-containing protein

G-patch domain-containing protein

RNA helicase

Putative cyclophilin protein

Unknown protein

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