SMTL ID : 8ch6.1

Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain K: C.11, I.45, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.11, K:C.46, K:C.49, K:C.85 ZN.2: 4 residues within 4Å: Chain K: C.30, C.33, C.72, C.75 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.30, K:C.33, K:C.72, K:C.75 ZN.3: 5 residues within 4Å: Chain K: C.23, C.26, C.58, I.60, C.61 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.23, K:C.26, K:C.58, K:C.61 ZN.4: 5 residues within 4Å: Chain P: C.56, L.58, C.59, H.72, H.78 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.56, P:C.59, P:H.72, P:H.78 ZN.5: 4 residues within 4Å: Chain Q: C.408, C.411, H.425, H.431 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.408, Q:C.411, Q:H.425, Q:H.431 ZN.6: 7 residues within 4Å: Chain 0: C.105, C.117, C.119, C.134, C.137 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.105, 0:C.117, 0:C.119, 0:C.134 ZN.7: 7 residues within 4Å: Chain 0: C.101, C.119, C.137, C.139, C.142 Ligands: ZN.6, ZN.8 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.101, 0:C.119, 0:C.139, 0:C.142 ZN.8: 6 residues within 4Å: Chain 0: C.101, C.102, C.105, C.137 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.101, 0:C.102, 0:C.105, 0:C.137 ZN.9: 5 residues within 4Å: Chain 1: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.24, 1:C.27, 1:C.81, 1:C.84 ZN.10: 5 residues within 4Å: Chain 1: C.45, C.48, R.50, C.71, C.74 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.45, 1:C.48, 1:C.71, 1:C.74 ZN.11: 5 residues within 4Å: Chain 1: C.165, C.173, G.176, C.179, H.183 5 PLIP interactions: 5 interactions with chain 1 Metal complexes: 1:C.165, 1:C.173, 1:C.179, 1:H.183, 1:H.183 ZN.12: 5 residues within 4Å: Chain 6: C.202, Y.205, C.211, C.217, H.221 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.202, 6:C.211, 6:C.217, 6:H.221

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.13: 10 residues within 4Å: Chain 7: K.442, Y.580, H.584, Q.587, K.609, H.610, Y.613, Y.614, K.623, N.1546 13 PLIP interactions: 13 interactions with chain 7 Hydrogen bonds: 7:H.610 Salt bridges: 7:K.442, 7:K.442, 7:K.442, 7:H.584, 7:H.584, 7:K.606, 7:K.609, 7:K.609, 7:K.609, 7:H.610, 7:K.623, 7:K.623

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

GTP.14: 21 residues within 4Å: Chain 8: H.137, L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, V.179, G.180, P.206, G.207, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.15 20 PLIP interactions: 20 interactions with chain 8 Hydrogen bonds: 8:H.139, 8:H.140, 8:G.141, 8:K.142, 8:T.143, 8:T.143, 8:C.144, 8:D.164, 8:G.180, 8:G.207, 8:K.259, 8:K.259, 8:S.312, 8:Q.313, 8:Q.313 Salt bridges: 8:H.139, 8:H.139, 8:K.142, 8:K.142, 8:D.261

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

MG.15: 2 residues within 4Å: Chain 8: T.143 Ligands: GTP.14 1 PLIP interactions: 1 interactions with chain 8 Metal complexes: 8:T.143 MG.16: 3 residues within 4Å: Ligands: MG.17 Chain a: G.54, U.74 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Ligands: MG.16 Chain a: G.46, G.54, A.73, U.74 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain a: G.75, A.76 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain a: G.71, G.72, G.75 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain 7: Q.675 Chain a: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.21: 5 residues within 4Å: Chain a: A.48, G.49, A.50, U.51, U.52 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitzova, J. et al., Structural basis of catalytic activation in human splicing. Nature (2023)

Release Date

2023-05-10

Peptides

Small nuclear ribonucleoprotein E: Af
Small nuclear ribonucleoprotein F: Be
Small nuclear ribonucleoprotein Sm D3: Cg
Small nuclear ribonucleoprotein Sm D2: Di
Small nuclear ribonucleoprotein Sm D1: Eh
Small nuclear ribonucleoprotein-associated proteins B and B': Fk
Small nuclear ribonucleoprotein G: Gj
Splicing factor 3B subunit 3: H
Splicing factor 3B subunit 5: I
Splicing factor 3B subunit 1: J
PHD finger-like domain-containing protein 5A: K
Splicing factor 3B subunit 2: L
Splicing factor 3B subunit 4: M
G-patch domain and KOW motifs-containing protein: N
Splicing factor 3A subunit 1: O
Splicing factor 3A subunit 2: P
Splicing factor 3A subunit 3: Q
Pre-mRNA-processing factor 19: RTYs
BUD13 homolog: S
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: U
Pleiotropic regulator 1: V
Cell division cycle 5-like protein: W
Spliceosome-associated protein CWC15 homolog: X
Pre-mRNA-splicing factor SPF27: Z
Protein BUD31 homolog: 0
Pre-mRNA-splicing factor RBM22: 1
Peptidyl-prolyl cis-trans isomerase-like 4: 2
Pre-mRNA-splicing factor CWC22 homolog: 3
Crooked neck-like protein 1: 4
SNW domain-containing protein 1: 5
RING finger protein 113A: 6
Pre-mRNA-processing-splicing factor 8: 7
116 kDa U5 small nuclear ribonucleoprotein component: 8
U5 small nuclear ribonucleoprotein 200 kDa helicase: 9
U5 small nuclear ribonucleoprotein 40 kDa protein: l
Peptidyl-prolyl cis-trans isomerase-like 1: m
Serine/arginine repetitive matrix protein 2: n
U2 small nuclear ribonucleoprotein A': o
U2 small nuclear ribonucleoprotein B'': p
Pre-mRNA-splicing factor ISY1 homolog: q
RING-type E3 ubiquitin-protein ligase PPIL2: r
Peptidyl-prolyl cis-trans isomerase E: t
Pre-mRNA-processing factor 17: u
Intron-binding protein aquarius: v
Pre-mRNA-splicing factor SYF1: w

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

f
i

B
2

e
h

C
3

g
j

D
4

i
l

E
5

h
k

F
8

k
n

G
9

j
m

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

T
M

Y
R

s
v

S
L

U
N

V
O

W
P

X
Q

Z
S

0
T

1
U

2
V

3
W

4
X

5
Y

6
Z

7
a

8
b

9
c

l
o

m
p

n
q

o
r

p
s

q
t

r
u

t
w

u
x

v
y

w
z

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein G

Splicing factor 3B subunit 3

Splicing factor 3B subunit 5

Splicing factor 3B subunit 1

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 2

Splicing factor 3B subunit 4

G-patch domain and KOW motifs-containing protein

Splicing factor 3A subunit 1

Splicing factor 3A subunit 2

Splicing factor 3A subunit 3

Pre-mRNA-processing factor 19

BUD13 homolog

Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16

Pleiotropic regulator 1

Cell division cycle 5-like protein

Spliceosome-associated protein CWC15 homolog

Pre-mRNA-splicing factor SPF27

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Peptidyl-prolyl cis-trans isomerase-like 4

Pre-mRNA-splicing factor CWC22 homolog

Crooked neck-like protein 1

SNW domain-containing protein 1

RING finger protein 113A

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

U5 small nuclear ribonucleoprotein 200 kDa helicase

U5 small nuclear ribonucleoprotein 40 kDa protein

Peptidyl-prolyl cis-trans isomerase-like 1

Serine/arginine repetitive matrix protein 2

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor ISY1 homolog

RING-type E3 ubiquitin-protein ligase PPIL2

Peptidyl-prolyl cis-trans isomerase E

Pre-mRNA-processing factor 17

Intron-binding protein aquarius

Pre-mRNA-splicing factor SYF1

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