SMTL ID : 5gmk.1

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

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

Ligands

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

GTP.1: 18 residues within 4Å: Chain B: L.142, H.143, G.145, K.146, T.147, S.148, R.176, L.189, S.190, G.217, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:H.143, B:G.145, B:K.146, B:T.147, B:T.147, B:S.148, B:S.148, B:R.176, B:S.190, B:G.217, B:K.269, B:R.272, B:S.315, B:T.316, B:K.317 Salt bridges: B:K.146, B:K.146, B:D.271

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

MG.2: 3 residues within 4Å: Chain B: T.147, S.190 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.147, B:S.190 MG.3: 4 residues within 4Å: Chain D: G.78, U.80 Chain G: G.13 Chain H: G.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain D: A.59, A.79, U.80 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain D: G.81 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain D: G.81 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain D: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain L: C.13, C.16, C.71, C.73, C.74 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.13, L:C.71, L:C.73, L:C.74 ZN.9: 4 residues within 4Å: Chain L: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.34, L:C.37, L:C.61, L:C.64 ZN.10: 4 residues within 4Å: Chain M: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.73, M:C.81, M:C.87, M:H.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: 5 residues within 4Å: Chain O: C.104, C.122, C.150, C.153 Ligands: ZN.11 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, C.148 Ligands: ZN.11 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 S: C.51, C.54, C.88, C.91 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.51, S:C.54, S:C.88, S:C.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, R. et al., Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution. Science (2016)

Release Date

2016-08-17

Peptides

Pre-mRNA-splicing factor 8: A
Pre-mRNA-splicing factor SNU114: B
Pre-mRNA-splicing factor CWC21: I
Pre-mRNA-splicing factor PRP46: J
Pre-mRNA-processing protein 45: K
Pre-mRNA-splicing factor SLT11: L
Pre-mRNA-splicing factor CWC2: M
Pre-mRNA-splicing factor CWC15: N
Pre-mRNA-splicing factor BUD31: O
Pre-mRNA-splicing factor CWC22: P
Pre-mRNA-splicing factor CEF1: Q
Pre-mRNA-splicing factor CLF1: R
Protein CWC16: S
Pre-mRNA-splicing factor CWC25: T
Pre-mRNA-splicing factor ISY1: U
Pre-mRNA-splicing factor SYF2: V
Pre-mRNA-splicing factor SYF1: W
Pre-mRNA-processing factor 17: X
Pre-mRNA-processing factor 19: YZ01
Pre-mRNA-splicing factor SNT309: 2
Small nuclear ribonucleoprotein-associated protein B: 3a
Small nuclear ribonucleoprotein E: 4b
Small nuclear ribonucleoprotein F: 5c
Small nuclear ribonucleoprotein G: 6d
Small nuclear ribonucleoprotein Sm D3: 7e
Small nuclear ribonucleoprotein Sm D1: 8f
Small nuclear ribonucleoprotein Sm D2: 9g
U2 small nuclear ribonucleoprotein B'': h
U2 small nuclear ribonucleoprotein A': i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

I
J

J
O

K
P

L
Q

M
R

N
S

O
T

P
Z

Q
c

R
d

S
F

T
G

U
H

V
I

W
v

X
n

Y
o

Z
p

0
q

1
r

2
t

3
k

a
s

4
i

b
u

5
h

c
w

6
j

d
x

7
l

e
y

8
m

f
z

9
g

g
e

h
a

i
b

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor PRP46

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor SLT11

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor CWC15

Pre-mRNA-splicing factor BUD31

Pre-mRNA-splicing factor CWC22

Pre-mRNA-splicing factor CEF1

Pre-mRNA-splicing factor CLF1

Protein CWC16

Pre-mRNA-splicing factor CWC25

Pre-mRNA-splicing factor ISY1

Pre-mRNA-splicing factor SYF2

Pre-mRNA-splicing factor SYF1

Pre-mRNA-processing factor 17

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SNT309

Small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

U2 small nuclear ribonucleoprotein B''

U2 small nuclear ribonucleoprotein A'

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