SMTL ID : 9l5t.1

Cryo-EM structure of the thermophile spliceosome (state B*Q2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-4-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-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 J: V.560 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 GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 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, N.300, K.301, D.303, R.304, C.355, T.356, S.357 21 PLIP interactions: 21 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:S.222, F:S.222, F:S.222, F:G.249, F:K.301, F:D.303, F:T.356, F:T.356, F:S.357 Salt bridges: F:H.174, F:K.177, F:K.177, F:D.303 pi-Cation interactions: F:K.301

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain S: C.103, C.104, C.107, C.139 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.103, S:C.104, S:C.107, S:C.139 ZN.4: 6 residues within 4Å: Chain S: C.103, C.121, C.141, C.144 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.103, S:C.121, S:C.141, S:C.144 ZN.5: 6 residues within 4Å: Chain S: C.107, C.119, C.121, C.136 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.107, S:C.119, S:C.121, S:C.136 ZN.6: 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 ZN.7: 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

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-splicing factor: N
Pre-mRNA-processing factor 19: OPQR
Putative bud site selection protein: S
Peptidyl-prolyl cis-trans isomerase: T
Pre-mRNA-splicing factor PRP46: 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
Small nuclear ribonucleoprotein E: 0
Small nuclear ribonucleoprotein G: 1
Sm protein F: 2
Delta(14)-sterol reductase: 3
Small nuclear ribonucleoprotein Sm D1: 4
Sm protein B: 5
Small nuclear ribonucleoprotein Sm D3: 6
GPATCH1: 7
RNA helicase: 8
Putative pre-mRNA splicing protein: 9
Putative pre-mRNA splicing protein: a
Nineteen complex-related protein 2-domain-containing protein: b
GCFC2: c
TFIP11: d
RNA helicase: f

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
Y

O
q

P
t

Q
r

R
s

S
N

T
S

U
T

V
M

W
0

X
R

Y
W

Z
P

0
j

1
k

2
l

3
m

4
o

5
p

6
u

7
1

8
z

9
V

a
Z

b
CY

c
Ck

d
Cb

f
Cc

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-splicing factor

Pre-mRNA-processing factor 19

Putative bud site selection protein

Peptidyl-prolyl cis-trans isomerase

Pre-mRNA-splicing factor PRP46

Putative pre-mRNA splicing protein

Putative pre-mRNA splicing protein

Pre-mRNA-processing protein 45

PRP17

Putative pre-mRNA splicing protein

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Sm protein F

Delta(14)-sterol reductase

Small nuclear ribonucleoprotein Sm D1

Sm protein B

Small nuclear ribonucleoprotein Sm D3

GPATCH1

RNA helicase

Putative pre-mRNA splicing protein

Putative pre-mRNA splicing protein

Nineteen complex-related protein 2-domain-containing protein

GCFC2

TFIP11

RNA helicase

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