SMTL ID : 7b9v.1

Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 5 residues within 4Å: Chain C: G.78, U.80 Chain H: G.47 Chain L: G.1 Ligands: MG.2 No protein-ligand interaction detected (PLIP) MG.2: 6 residues within 4Å: Chain C: A.59, G.60, U.80 Chain L: G.1, A.70 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain C: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain C: G.81 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: A.62, U.80, G.81 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain F: T.147, D.179, S.190 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.147, F:S.190

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

K.6: 4 residues within 4Å: Chain C: G.52, A.59, G.60, U.80 No protein-ligand interaction detected (PLIP)

1 x KGN: D-chiro inositol hexakisphosphate(Non-covalent)

KGN.7: 10 residues within 4Å: Chain D: R.236, K.517, H.659, K.684, H.685, Y.688, Y.689, N.692, K.697, G.698 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.688, D:Y.689, D:G.698 Salt bridges: D:K.228, D:R.236, D:K.517, D:K.517, D:K.517, D:H.659, D:H.659, D:K.684, D:K.684, D:K.684, D:H.685, D:K.697, D:K.697

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

GTP.9: 21 residues within 4Å: Chain F: L.142, H.143, S.144, G.145, K.146, T.147, S.148, P.174, L.189, S.190, P.216, G.217, H.218, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.8 23 PLIP interactions: 23 interactions with chain F Hydrogen bonds: F:H.143, F:S.144, F:G.145, F:K.146, F:T.147, F:T.147, F:T.147, F:S.148, F:S.190, F:S.190, F:G.217, F:H.218, F:N.268, F:K.269, F:K.269, F:T.316, F:T.316, F:K.317 Salt bridges: F:H.143, F:K.146, F:K.146, F:D.271 pi-Cation interactions: F:K.269

8 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain G: C.51, C.54, C.88, C.91 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.51, G:C.54, G:C.88, G:C.91 ZN.11: 6 residues within 4Å: Chain O: C.104, C.105, C.108, C.148 Ligands: ZN.12, ZN.13 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.104, O:C.105, O:C.108, O:C.148 ZN.12: 6 residues within 4Å: Chain O: C.104, C.122, C.150, C.153 Ligands: ZN.11, ZN.13 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.104, O:C.122, O:C.150, O:C.153 ZN.13: 6 residues within 4Å: Chain O: C.108, C.120, C.122, C.145 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.108, O:C.120, O:C.122, O:C.145 ZN.14: 4 residues within 4Å: Chain P: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.73, P:C.81, P:C.87, P:H.91 ZN.15: 4 residues within 4Å: Chain Q: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.34, Q:C.37, Q:C.61, Q:C.64 ZN.16: 4 residues within 4Å: Chain Q: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.13, Q:C.16, Q:C.71, Q:C.74 ZN.17: 4 residues within 4Å: Chain 3: C.122, C.125, H.130, C.135 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:C.122, 3:C.125, 3:H.130, 3:C.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkinson, M.E. et al., Structural basis for conformational equilibrium of the catalytic spliceosome. Mol.Cell (2021)

Release Date

2021-03-10

Peptides

Pre-mRNA-splicing factor 8: D
Pre-mRNA-splicing helicase BRR2: E
Pre-mRNA-splicing factor SNU114: F
Splicing factor YJU2: G
Pre-mRNA-splicing factor CWC25: I
Pre-mRNA-splicing factor ISY1: J
CWC22 isoform 1: K
BJ4_G0054360.mRNA.1.CDS.1: M
Pre-mRNA-processing protein 45: N
BUD31 isoform 1: O
Pre-mRNA-splicing factor CWC2: P
Pre-mRNA-splicing factor SLT11: Q
Y55_G0042700.mRNA.1.CDS.1: R
Pre-mRNA-splicing factor CWC15: S
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16: T
Pre-mRNA-splicing factor CWC21: U
CLF1 isoform 1: V
SYF1 isoform 1: W
HLJ1_G0053790.mRNA.1.CDS.1: X
Unassigned structure: Y
BJ4_G0027490.mRNA.1.CDS.1: Z
NTC20 isoform 1: 0
Pre-mRNA-splicing factor 18: 1
Small nuclear ribonucleoprotein-associated protein B: 2a
Pre-mRNA-splicing factor SLU7: 3
Small nuclear ribonucleoprotein Sm D3: 4d
Small nuclear ribonucleoprotein E: 5f
Small nuclear ribonucleoprotein F: 6g
Small nuclear ribonucleoprotein G: 7h
Small nuclear ribonucleoprotein Sm D1: 8b
Small nuclear ribonucleoprotein Sm D2: 9c
CDC40 isoform 1: e
SNT309 isoform 1: i
Pre-mRNA-processing factor 19: jklm
Pre-mRNA-splicing factor SYF2: n

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
D

I
F

J
G

K
H

M
J

N
K

O
L

P
M

Q
N

R
O

S
P

T
Q

U
R

V
S

W
T

X
W

Y
X

Z
Y

0
Z

1
a

2
b

a
k

3
c

4
d

d
n

5
e

f
p

6
f

g
q

7
g

h
r

8
h

b
l

9
j

c
m

e
o

i
s

j
t

k
u

l
v

m
w

n
y

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing helicase BRR2

Pre-mRNA-splicing factor SNU114

Splicing factor YJU2

Pre-mRNA-splicing factor CWC25

Pre-mRNA-splicing factor ISY1

CWC22 isoform 1

BJ4_G0054360.mRNA.1.CDS.1

Pre-mRNA-processing protein 45

BUD31 isoform 1

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor SLT11

Y55_G0042700.mRNA.1.CDS.1

Pre-mRNA-splicing factor CWC15

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

Pre-mRNA-splicing factor CWC21

CLF1 isoform 1

SYF1 isoform 1

HLJ1_G0053790.mRNA.1.CDS.1

Unassigned structure

BJ4_G0027490.mRNA.1.CDS.1

NTC20 isoform 1

Pre-mRNA-splicing factor 18

Small nuclear ribonucleoprotein-associated protein B

Pre-mRNA-splicing factor SLU7

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

CDC40 isoform 1

SNT309 isoform 1

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SYF2

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