SMTL ID : 8ro0.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 3 residues within 4Å: Chain C: G.49, C.50, G.66 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain C: G.41, A.48, G.49, U.69 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain C: A.43, A.45, U.47 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain C: G.66, U.69, G.70 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain C: G.70 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: G.66, G.67, U.69 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain F: T.146, S.183, D.207, T.208 Ligands: GTP.8 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.146, F:S.183

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.7: 6 residues within 4Å: Chain D: K.434, H.576, K.598, K.601, K.615, N.1539 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.1539 Salt bridges: D:K.434, D:K.434, D:H.576, D:K.598, D:K.598, D:K.598, D:K.601, D:K.601, D:K.615, D:K.615 IHP.10: 11 residues within 4Å: Chain J: K.373, R.377, F.418, A.419, K.420, K.451, D.452, K.453 Chain L: K.307 Chain X: K.118, K.124 20 PLIP interactions: 2 interactions with chain L, 14 interactions with chain J, 4 interactions with chain X Salt bridges: L:K.307, L:K.307, J:K.373, J:K.373, J:R.377, J:K.420, J:K.420, J:K.451, J:K.451, J:K.451, J:K.453, J:K.453, J:K.453, X:K.118, X:K.118, X:K.124, X:K.124 Hydrogen bonds: J:A.419, J:K.420, J:K.453

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

GTP.8: 22 residues within 4Å: Chain D: P.325 Chain F: H.140, L.141, H.142, H.143, G.144, K.145, T.146, T.147, D.167, R.169, C.182, S.183, T.208, G.210, K.262, D.264, R.265, S.314, G.315, R.316 Ligands: MG.9 21 PLIP interactions: 21 interactions with chain F Hydrogen bonds: F:H.142, F:H.143, F:G.144, F:K.145, F:T.146, F:T.147, F:T.147, F:D.167, F:S.183, F:S.183, F:S.183, F:G.210, F:S.314, F:G.315, F:R.316, F:R.316 Salt bridges: F:H.142, F:H.142, F:K.145, F:K.145, F:D.264

6 x ZN: ZINC ION(Non-covalent)

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

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
U5 small nuclear ribonucleoprotein 200 kDa helicase: E
Tr-type G domain-containing protein: F
Protein isy-1: G
WD_REPEATS_REGION domain-containing protein: H
Pre-mRNA-splicing factor SYF1: I
TPR_REGION domain-containing protein: J
Pre-mRNA-splicing factor SPF27: K
Cell division cycle 5-like protein: L
Pre-mRNA-splicing factor syf-2: M
Protein BUD31 homolog: N
Pre-mRNA-splicing factor RBM22: O
Spliceosome-associated protein CWC15 homolog: P
GCF C-terminal domain-containing protein: Q
Intron-binding protein aquarius: R
Uncharacterized protein T27F2.1: S
Peptidyl-prolyl cis-trans isomerase: T
WD_REPEATS_REGION domain-containing protein: U
Septin and tuftelin-interacting protein 1 homolog: V
WD_REPEATS_REGION domain-containing protein: W
Coiled-coil domain-containing protein 12: X
Small nuclear ribonucleoprotein Sm D3: Y5
Probable small nuclear ribonucleoprotein-associated protein B: Z6
Small nuclear ribonucleoprotein Sm D1: 07
Probable small nuclear ribonucleoprotein Sm D2: 18
Probable small nuclear ribonucleoprotein E: 29
Probable small nuclear ribonucleoprotein F: 3a
Probable small nuclear ribonucleoprotein G: 4b
Probable U2 small nuclear ribonucleoprotein A': c
RRM domain-containing protein: d
Pre-mRNA-processing factor 19: efgh
Peptidyl-prolyl cis-trans isomerase E: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
D

H
E

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
PX

R
Q

S
R

T
S

U
T

V
TF

W
W

X
Z

Y
a

5
h

Z
b

6
i

0
c

7
j

1
d

8
k

2
e

9
l

3
f

a
m

4
g

b
n

c
o

d
p

e
q

f
r

g
s

h
t

i
y

Pre-mRNA-splicing factor 8 homolog

U5 small nuclear ribonucleoprotein 200 kDa helicase

Tr-type G domain-containing protein

Protein isy-1

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

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

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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