SMTL ID : 5gm6.1

Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

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

Ligands

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

GTP.1: 17 residues within 4Å: Chain C: H.143, S.144, G.145, K.146, T.147, S.148, R.176, L.189, S.190, P.216, G.217, H.218, K.269, D.271, S.315, T.316, K.317 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:H.143, C:S.144, C:G.145, C:K.146, C:T.147, C:T.147, C:S.148, C:S.148, C:S.190, C:S.190, C:S.190, C:S.190, C:G.217, C:H.218, C:K.269, C:T.316, C:K.317 Salt bridges: C:H.143, C:K.146, C:K.146, C:D.271 pi-Cation interactions: C:K.269

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

MG.2: 4 residues within 4Å: Chain E: A.59, G.60, U.80 Chain L: G.11 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain E: G.81 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain E: G.81, A.82 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain E: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain W: K.252, T.253, D.346 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:T.253

13 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain H: C.68, C.71, H.84, H.90 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.68, H:C.71, H:H.84, H:H.90 ZN.7: 4 residues within 4Å: Chain I: C.11, C.46, C.49, C.86 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.11, I:C.46, I:C.49, I:C.86 ZN.8: 4 residues within 4Å: Chain I: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.23, I:C.26, I:C.58, I:C.61 ZN.9: 4 residues within 4Å: Chain I: C.30, C.33, C.73, C.76 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.30, I:C.33, I:C.73, I:C.76 ZN.10: 5 residues within 4Å: Chain P: C.13, C.16, C.71, C.73, C.74 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.13, P:C.71, P:C.73, P:C.74 ZN.11: 4 residues within 4Å: Chain P: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.34, P:C.37, P:C.61, P:C.64 ZN.12: 4 residues within 4Å: Chain Q: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.73, Q:C.81, Q:C.87, Q:H.91 ZN.13: 6 residues within 4Å: Chain S: C.104, C.105, C.108, C.148 Ligands: ZN.14, ZN.15 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.104, S:C.105, S:C.108, S:C.148 ZN.14: 6 residues within 4Å: Chain S: C.104, C.122, C.150, C.153 Ligands: ZN.13, ZN.15 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.104, S:C.122, S:C.150, S:C.153 ZN.15: 7 residues within 4Å: Chain S: C.108, C.120, C.122, C.145, C.148 Ligands: ZN.13, ZN.14 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.108, S:C.120, S:C.122, S:C.145 ZN.18: 4 residues within 4Å: Chain Y: C.144, C.153, C.159, H.163 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.144, Y:C.153, Y:C.159, Y:H.163 ZN.19: 4 residues within 4Å: Chain Y: C.199, C.202, C.219, C.222 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.199, Y:C.202, Y:C.219, Y:C.222 ZN.20: 4 residues within 4Å: Chain Y: C.214, H.216, C.233, C.236 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.214, Y:H.216, Y:C.233, Y:C.236

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.17: 13 residues within 4Å: Chain W: L.223, G.249, S.250, G.251, K.252, T.253, T.254, R.289, F.487, T.509, D.511, R.555 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain W Hydrogen bonds: W:G.249, W:G.249, W:S.250, W:G.251, W:K.252, W:T.253, W:T.254, W:T.509, W:R.555 Salt bridges: W:K.252 pi-Cation interactions: W:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, C. et al., Structure of a yeast activated spliceosome at 3.5 angstrom resolution. Science (2016)

Release Date

2016-09-21

Peptides

Pre-mRNA-splicing factor 8: A
Pre-mRNA-splicing helicase BRR2: B
Pre-mRNA-splicing factor SNU114: C
Pre-mRNA-splicing factor RSE1: F
Cold sensitive U2 snRNA suppressor 1: G
Pre-mRNA-splicing factor PRP11: H
Pre-mRNA-splicing factor RDS3: I
RDS3 complex subunit 10: J
Pre-mRNA-splicing factor PRP46: N
Pre-mRNA-processing protein 45: O
Pre-mRNA-splicing factor SLT11: P
Pre-mRNA-splicing factor CWC2: Q
Pre-mRNA-splicing factor CWC15: R
Pre-mRNA-splicing factor BUD31: S
Pre-mRNA leakage protein 1: T
U2 snRNP component IST3: U
Pre-mRNA-splicing factor CWC26: V
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2: W
Pre-mRNA-splicing factor CWC22: X
Pre-mRNA-splicing factor CWC24: Y
Peptidyl-prolyl isomerase CWC27: Z
Pre-mRNA-splicing factor CEF1: 0
U2 snRNP component HSH155: 1
Pre-mRNA-splicing factor CLF1: 2
Pre-mRNA-splicing factor CWC21: 3
Pre-mRNA-splicing factor SYF1: 4
Protein HSH49: 5
Pre-mRNA-splicing factor SYF2: 6
Pre-mRNA-processing factor 19: 789a
Pre-mRNA-splicing factor SNT309: b
Pre-mRNA-processing factor 17: c
Small nuclear ribonucleoprotein-associated protein B: d
Small nuclear ribonucleoprotein E: e
Small nuclear ribonucleoprotein F: f
Small nuclear ribonucleoprotein G: g
Small nuclear ribonucleoprotein Sm D3: h
Small nuclear ribonucleoprotein Sm D1: i
Small nuclear ribonucleoprotein Sm D2: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

F
F

G
H

H
I

I
J

J
K

N
O

O
P

P
Q

Q
R

R
S

S
T

T
U

U
V

V
W

W
Y

X
Z

Y
a

Z
b

0
c

1
G

2
d

3
X

4
v

5
e

6
f

7
o

8
p

9
q

a
r

b
t

c
n

d
k

e
i

f
h

g
j

h
l

i
m

j
g

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing helicase BRR2

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor RSE1

Cold sensitive U2 snRNA suppressor 1

Pre-mRNA-splicing factor PRP11

Pre-mRNA-splicing factor RDS3

RDS3 complex subunit 10

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 leakage protein 1

U2 snRNP component IST3

Pre-mRNA-splicing factor CWC26

Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2

Pre-mRNA-splicing factor CWC22

Pre-mRNA-splicing factor CWC24

Peptidyl-prolyl isomerase CWC27

Pre-mRNA-splicing factor CEF1

U2 snRNP component HSH155

Pre-mRNA-splicing factor CLF1

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor SYF1

Protein HSH49

Pre-mRNA-splicing factor SYF2

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SNT309

Pre-mRNA-processing factor 17

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

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