SMTL ID : 8ro1.1

Structure of the C. elegans Intron Lariat Spliceosome double-primed for disassembly (ILS'')

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 3 residues within 4Å: Chain C: U.69, G.70 Ligands: MG.2 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain C: G.70 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain C: G.67, A.68, U.69 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain C: C.50, G.66 Chain D: Q.667 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: A.42, A.43, U.47 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: A.48, G.49, U.69 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain E: K.145, T.146, S.183, D.207 Ligands: GTP.8 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.146, E:S.183, E:D.207

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)(Covalent)

IHP.7: 10 residues within 4Å: Chain D: R.153, K.434, H.576, K.598, K.601, H.602, Y.605, N.609, K.615, G.616 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.605, D:N.609, D:G.616 Salt bridges: D:R.153, D:K.434, D:K.434, D:H.576, D:K.598, D:K.601, D:K.601, D:K.601, D:H.602, D:K.615 IHP.10: 14 residues within 4Å: Chain 1: K.35, D.37 Chain K: K.373, R.377, Y.381, T.417, F.418, A.419, K.420, K.451, D.452, K.453, R.456 Chain M: K.307 18 PLIP interactions: 1 interactions with chain 1, 14 interactions with chain K, 3 interactions with chain M Salt bridges: 1:K.35, K:K.373, K:K.373, K:K.420, K:K.420, K:K.420, K:K.451, K:K.451, K:K.453, K:R.456, M:K.307, M:K.307, M:K.307 Hydrogen bonds: K:R.377, K:Y.381, K:A.419, K:K.420, K:K.453

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.8: 23 residues within 4Å: Chain D: P.325 Chain E: H.140, L.141, H.142, H.143, G.144, K.145, T.146, T.147, D.167, R.169, G.181, C.182, S.183, G.210, K.262, D.264, R.265, E.269, S.314, G.315, R.316 Ligands: MG.9 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:H.142, E:K.145, E:T.146, E:T.147, E:T.147, E:D.167, E:S.183, E:S.183, E:S.183, E:G.210, E:K.262, E:E.269, E:R.316, E:R.316 Salt bridges: E:H.142, E:K.145, E:K.145, E:K.262, E:D.264 pi-Cation interactions: E:K.262, E:R.316

7 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain O: C.239, C.242, H.282, H.329 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.239, O:C.242, O:H.282, O:H.329 ZN.12: 6 residues within 4Å: Chain Q: C.108, C.120, C.122, C.137 Ligands: ZN.13, ZN.14 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.108, Q:C.120, Q:C.122, Q:C.137 ZN.13: 5 residues within 4Å: Chain Q: C.104, C.105, C.108, C.140 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.104, Q:C.105, Q:C.108, Q:C.140 ZN.14: 5 residues within 4Å: Chain Q: C.104, C.122, C.142, C.145 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.104, Q:C.122, Q:C.142, Q:C.145 ZN.15: 4 residues within 4Å: Chain R: C.25, C.28, C.82, C.85 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.25, R:C.28, R:C.82, R:C.85 ZN.16: 4 residues within 4Å: Chain R: C.46, C.49, C.72, C.75 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.46, R:C.49, R:C.72, R:C.75 ZN.17: 4 residues within 4Å: Chain R: C.168, C.176, C.182, H.186 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.168, R:C.176, R:C.182, R:H.186

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

2024-08-07

Peptides

Pre-mRNA-splicing factor 8 homolog: D
Tr-type G domain-containing protein: E
Protein isy-1: F
Pre-mRNA-splicing factor ATP-dependent RNA helicase ddx-15: G
WD_REPEATS_REGION domain-containing protein: H
Pre-mRNA-splicing factor SYF1: I
TPR_REGION domain-containing protein: K
Pre-mRNA-splicing factor SPF27: L
Cell division cycle 5-like protein: M
CWF19-like protein 1 homolog: N
CWF19-like protein 2 homolog: O
Pre-mRNA-splicing factor syf-2: P
Protein BUD31 homolog: Q
Pre-mRNA-splicing factor RBM22: R
Spliceosome-associated protein CWC15 homolog: S
GCF C-terminal domain-containing protein: T
Intron-binding protein aquarius: U
Uncharacterized protein T27F2.1: V
Peptidyl-prolyl cis-trans isomerase: W
WD_REPEATS_REGION domain-containing protein: X
Septin and tuftelin-interacting protein 1 homolog: Y
WD_REPEATS_REGION domain-containing protein: Z
Replication stress response regulator SDE2: 0
Coiled-coil domain-containing protein 12: 1
Small nuclear ribonucleoprotein Sm D3: 29
Probable small nuclear ribonucleoprotein-associated protein B: 3a
Small nuclear ribonucleoprotein Sm D1: 4b
Probable small nuclear ribonucleoprotein Sm D2: 5c
Probable small nuclear ribonucleoprotein E: 6d
Probable small nuclear ribonucleoprotein F: 7e
Probable small nuclear ribonucleoprotein G: 8f
Probable U2 small nuclear ribonucleoprotein A': g
RRM domain-containing protein: h
Pre-mRNA-processing factor 19: ijkl
Peptidyl-prolyl cis-trans isomerase E: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
C

F
D

G
DX

H
E

I
I

K
J

L
K

M
L

N
L1

O
L2

P
M

Q
N

R
O

S
P

T
PX

U
Q

V
R

W
S

X
T

Y
TF

Z
W

0
X

1
Z

2
a

9
h

3
b

a
i

4
c

b
j

5
d

c
k

6
e

d
l

7
f

e
m

8
g

f
n

g
o

h
p

i
q

j
r

k
s

l
t

m
y

Pre-mRNA-splicing factor 8 homolog

Tr-type G domain-containing protein

Protein isy-1

Pre-mRNA-splicing factor ATP-dependent RNA helicase ddx-15

WD_REPEATS_REGION domain-containing protein

Pre-mRNA-splicing factor SYF1

TPR_REGION domain-containing protein

Pre-mRNA-splicing factor SPF27

Cell division cycle 5-like protein

CWF19-like protein 1 homolog

CWF19-like protein 2 homolog

Pre-mRNA-splicing factor syf-2

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Spliceosome-associated protein CWC15 homolog

GCF C-terminal domain-containing protein

Intron-binding protein aquarius

Uncharacterized protein T27F2.1

Peptidyl-prolyl cis-trans isomerase

WD_REPEATS_REGION domain-containing protein

Septin and tuftelin-interacting protein 1 homolog

WD_REPEATS_REGION domain-containing protein

Replication stress response regulator SDE2

Coiled-coil domain-containing protein 12

Small nuclear ribonucleoprotein Sm D3

Probable small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein Sm D1

Probable small nuclear ribonucleoprotein Sm D2

Probable small nuclear ribonucleoprotein E

Probable small nuclear ribonucleoprotein F

Probable small nuclear ribonucleoprotein G

Probable U2 small nuclear ribonucleoprotein A'

RRM domain-containing protein

Pre-mRNA-processing factor 19

Peptidyl-prolyl cis-trans isomerase E

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