SMTL ID : 6j6q.1

Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.70 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain A: R.236, K.517, H.659, K.684, H.685, Y.688, Y.689, N.692, K.697, G.698 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.698 Salt bridges: A:K.228, A:R.236, A:K.517, A:K.517, A:K.517, A:H.659, A:K.684, A:K.684, A:K.684, A:H.685

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

GTP.2: 21 residues within 4Å: Chain A: P.406 Chain B: L.142, H.143, S.144, G.145, K.146, T.147, S.148, R.176, L.189, S.190, P.216, G.217, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:H.143, B:S.144, B:G.145, B:K.146, B:T.147, B:T.147, B:S.148, B:S.148, B:S.190, B:G.217, B:K.269, B:T.316, B:K.317 Salt bridges: B:H.143, B:K.146, B:K.146, B:D.271

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

MG.3: 3 residues within 4Å: Chain B: T.147, S.190 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.147, B:S.190 MG.10: 5 residues within 4Å: Chain P: G.131, G.132 Chain R: G.77, G.78, U.80 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain R: A.59, G.60, A.79, U.80 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain R: G.81 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain R: G.81 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: Q.748 Chain R: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain F: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.13, F:C.16, F:C.71, F:C.74 ZN.5: 4 residues within 4Å: Chain F: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.34, F:C.37, F:C.61, F:C.64 ZN.6: 4 residues within 4Å: Chain G: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.73, G:C.81, G:C.87, G:H.91 ZN.7: 6 residues within 4Å: Chain I: C.104, C.105, C.108, C.148 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.104, I:C.105, I:C.108, I:C.148 ZN.8: 6 residues within 4Å: Chain I: C.104, C.122, C.150, C.153 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.104, I:C.122, I:C.150, I:C.153 ZN.9: 6 residues within 4Å: Chain I: C.108, C.120, C.122, C.145 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.108, I:C.120, I:C.122, I:C.145 ZN.15: 4 residues within 4Å: Chain f: C.51, C.54, C.88, C.91 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.51, f:C.54, f:C.88, f:C.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, R. et al., Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell (2019)

Release Date

2019-04-24

Peptides

Pre-mRNA-splicing factor 8: A
Pre-mRNA-splicing factor SNU114: B
Pre-mRNA-splicing factor CWC21: C
Pre-mRNA-splicing factor PRP46: D
Pre-mRNA-processing protein 45: E
Pre-mRNA-splicing factor SLT11: F
Pre-mRNA-splicing factor CWC2: G
Pre-mRNA-splicing factor CWC15: H
Pre-mRNA-splicing factor BUD31: I
Pre-mRNA-splicing factor CWC22: J
Pre-mRNA-splicing factor CEF1: K
Pre-mRNA-splicing factor CLF1: L
Pre-mRNA-splicing factor SYF2: M
Pre-mRNA-processing factor 17: N
Pre-mRNA-splicing factor ISY1: O
Pre-mRNA-splicing factor SYF1: T
U2 small nuclear ribonucleoprotein B'': U
U2 small nuclear ribonucleoprotein A': V
Pre-mRNA-splicing factor SNT309: W
Small nuclear ribonucleoprotein E: X6
Small nuclear ribonucleoprotein Sm D1: Ya
Small nuclear ribonucleoprotein G: Z8
Small nuclear ribonucleoprotein F: 07
Small nuclear ribonucleoprotein Sm D2: 13
Small nuclear ribonucleoprotein-associated protein B: 24
Small nuclear ribonucleoprotein Sm D3: 59
Pre-mRNA-processing factor 19: bcde
Splicing factor YJU2: f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
J

D
O

E
P

F
Q

G
R

H
S

I
T

J
Z

K
c

L
d

M
I

N
n

O
H

T
v

U
a

V
b

W
t

X
u

6
i

Y
m

a
z

Z
j

8
x

0
h

7
w

1
g

3
e

2
k

4
s

5
l

9
y

b
r

c
p

d
q

e
o

f
F

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

Pre-mRNA-splicing factor SYF2

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor ISY1

Pre-mRNA-splicing factor SYF1

U2 small nuclear ribonucleoprotein B''

U2 small nuclear ribonucleoprotein A'

Pre-mRNA-splicing factor SNT309

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein Sm D3

Pre-mRNA-processing factor 19

Splicing factor YJU2

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