SMTL ID : 9l5s.1

Cryo-EM structure of the thermophile spliceosome (state B*Q1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

M7M.1: 7 residues within 4Å: Chain A: A.1 Chain E: R.150, W.154, E.158, A.159, W.162, R.165 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:E.158, E:R.165 Salt bridges: 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: 5 residues within 4Å: Chain F: T.178, S.222, D.246, T.247 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: 21 residues within 4Å: Chain D: P.449 Chain F: L.173, H.174, H.175, G.176, K.177, T.178, A.179, Q.206, L.221, S.222, P.248, G.249, H.250, K.301, D.303, R.304, C.355, T.356, S.357 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain F Hydrogen bonds: F:H.174, F:H.175, F:G.176, F:K.177, F:T.178, F:T.178, F:A.179, F:Q.206, F:S.222, F:S.222, F:G.249, F:H.250, F:K.301, 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

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain Q: C.103, C.104, C.107, C.139 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.103, Q:C.104, Q:C.107, Q:C.139 ZN.5: 5 residues within 4Å: Chain Q: C.103, C.121, C.141, C.144 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.103, Q:C.121, Q:C.141, Q:C.144 ZN.6: 6 residues within 4Å: Chain Q: C.107, C.119, C.121, C.136 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.107, Q:C.119, Q:C.121, Q:C.136 ZN.7: 4 residues within 4Å: Chain T: C.23, C.26, C.82, C.85 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.23, T:C.26, T:C.82, T: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
Anaphase-promoting complex subunit 4-like WD40 domain-containing protein: G
CCDC12: H
Putative pre-mRNA splicing protein: I
Suppressor of forked domain-containing protein: J
Putative pre-mRNA splicing protein: K
Pre-mRNA-splicing factor SPF27: L
Pre-mRNA-processing factor 19: MNOP
Putative bud site selection protein: Q
Peptidyl-prolyl cis-trans isomerase: R
Pre-mRNA-splicing factor PRP46: S
Putative pre-mRNA splicing protein: T
Putative pre-mRNA splicing protein: U
Pre-mRNA-processing protein 45: V
PRP17: W
Putative pre-mRNA splicing protein: X
Pre-mRNA-splicing factor: Y
GPATCH1: Z
RNA helicase: 0
Small nuclear ribonucleoprotein E: 1
Small nuclear ribonucleoprotein G: 2
Sm protein F: 3
Delta(14)-sterol reductase: 4
Small nuclear ribonucleoprotein Sm D1: 5
Sm protein B: 6
Small nuclear ribonucleoprotein Sm D3: 7
Putative pre-mRNA splicing protein: 8
Putative pre-mRNA splicing protein: 9
Nineteen complex-related protein 2-domain-containing protein: a
GCFC2: b
TFIP11: c
Putative pre-mRNA splicing protein: e

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
E

H
F

I
I

J
J

K
L

L
K

M
q

N
t

O
r

P
s

Q
N

R
S

S
T

T
M

U
0

V
R

W
W

X
P

Y
Y

Z
1

0
z

1
j

2
k

3
l

4
m

5
o

6
p

7
u

8
V

9
Z

a
CY

b
Ck

c
Cb

e
CV

PRP8

Pre-mRNA-splicing factor SYF2

SNU114

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

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

GPATCH1

RNA helicase

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

Putative pre-mRNA splicing protein

Putative pre-mRNA splicing protein

Nineteen complex-related protein 2-domain-containing protein

GCFC2

TFIP11

Putative pre-mRNA splicing protein

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