SMTL ID : 9esi.1

Structure of a B-state intermediate committed to discard (Bd-II state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain E: R.184, K.465, H.607, K.632, H.633, Y.636, Y.637, N.640, K.646, G.647 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.636, E:N.640, E:G.647, E:G.647 Salt bridges: E:R.184, E:K.465, E:K.465, E:K.465, E:H.607, E:H.607, E:K.632, E:K.632, E:K.632, E:H.633, E:K.646, E:K.646

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

GTP.2: 21 residues within 4Å: Chain F: H.149, L.150, H.151, H.152, G.153, K.154, S.155, A.156, S.176, R.178, M.191, S.192, G.219, N.270, K.271, D.273, R.274, S.323, C.324, D.325 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:H.151, F:H.152, F:G.153, F:K.154, F:S.155, F:A.156, F:S.192, F:S.192, F:G.219, F:N.270, F:K.271, F:K.271, F:C.324, F:D.325 Salt bridges: F:H.151, F:K.154, F:K.154, F:D.273, F:D.325

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

MG.3: 4 residues within 4Å: Chain F: S.155, S.192, D.216 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.155, F:S.192 MG.10: 2 residues within 4Å: Chain e: C.49, G.65 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain e: G.65, U.68, G.69 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain e: G.69 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain Q: C.23, C.26, C.80, S.82, C.83 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.23, Q:C.26, Q:C.80, Q:C.83 ZN.5: 5 residues within 4Å: Chain Q: C.44, C.47, C.70, C.73, Q.121 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.44, Q:C.47, Q:C.70, Q:C.73 ZN.6: 6 residues within 4Å: Chain S: C.101, C.102, C.105, C.137 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.101, S:C.102, S:C.105, S:C.137 ZN.7: 6 residues within 4Å: Chain S: C.101, C.119, C.139, C.142 Ligands: ZN.6, ZN.8 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.101, S:C.119, S:C.139, S:C.142 ZN.8: 6 residues within 4Å: Chain S: C.105, C.117, C.119, C.134 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.105, S:C.117, S:C.119, S:C.134 ZN.9: 6 residues within 4Å: Chain T: C.117, C.125, E.127, C.131, Y.133, H.135 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.117, T:C.125, T:C.131, T:H.135

1 x K: POTASSIUM ION(Non-functional Binders)

K.12: 3 residues within 4Å: Chain e: G.40, G.48, U.68 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soni, K. et al., Structures of aberrant spliceosome intermediates on their way to disassembly. To Be Published

Release Date

2024-12-25

Peptides

Stress response protein bis1: A
Protein saf4: B
Pre-mRNA-splicing factor spp42: E
Pre-mRNA-splicing factor cwf10: F
Pre-mRNA-splicing factor cwf17: G
Small nuclear ribonucleoprotein Sm D3: H
Small nuclear ribonucleoprotein-associated protein B: I
Small nuclear ribonucleoprotein Sm D1: J
Small nuclear ribonucleoprotein Sm D2: K
Small nuclear ribonucleoprotein E: L
Small nuclear ribonucleoprotein F: M
Small nuclear ribonucleoprotein G: N
Pre-mRNA-splicing factor prp5: O
Pre-mRNA-processing protein 45: P
Pre-mRNA-splicing factor cwf5: Q
Pre-mRNA-splicing factor cwf11: R
Pre-mRNA-splicing factor cwf14: S
Pre-mRNA-splicing factor cwf2: T
Pre-mRNA-splicing factor cwf15: U
Pre-mRNA-splicing factor cwf4: V
Pre-mRNA-processing factor 19: WXYZ
Pre-mRNA-splicing factor cdc5: 0
Pre-mRNA-splicing factor cwf3: 1
Pre-mRNA-splicing factor syf2: 2
Pre-mRNA-splicing factor cwf7: 3
Pre-mRNA-processing factor 17: 4
Pre-mRNA-splicing factor cwf21: 5
Pre-mRNA-splicing factor cwf22: 6
Peptidyl-prolyl cis-trans isomerase ppi1: 7
G-patch domain-containing protein C1486.03: 8
Uncharacterized protein C17A2.08c: 9
Uncharacterized protein C20H4.06c: a
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09: b
UNK1: c
UNK2: d
UNK3: g

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
e

B
p

E
A

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

V
R

W
S

X
T

Y
U

Z
V

0
W

1
X

2
Y

3
Z

4
a

5
b

6
c

7
d

8
m

9
n

a
y

b
z

c
r

d
q

g
f

Stress response protein bis1

Protein saf4

Pre-mRNA-splicing factor spp42

Pre-mRNA-splicing factor cwf10

Pre-mRNA-splicing factor cwf17

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Pre-mRNA-splicing factor prp5

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor cwf5

Pre-mRNA-splicing factor cwf11

Pre-mRNA-splicing factor cwf14

Pre-mRNA-splicing factor cwf2

Pre-mRNA-splicing factor cwf15

Pre-mRNA-splicing factor cwf4

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor cdc5

Pre-mRNA-splicing factor cwf3

Pre-mRNA-splicing factor syf2

Pre-mRNA-splicing factor cwf7

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor cwf21

Pre-mRNA-splicing factor cwf22

Peptidyl-prolyl cis-trans isomerase ppi1

G-patch domain-containing protein C1486.03

Uncharacterized protein C17A2.08c

Uncharacterized protein C20H4.06c

Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09

UNK1

UNK2

UNK3

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