SMTL ID : 6bk8.1

S. cerevisiae spliceosomal post-catalytic P complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 4 residues within 4Å: Chain C: G.78, U.80 Chain D: A.13, G.14 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain C: G.81 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain C: G.81 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain C: C.61, A.76, G.77 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain G: T.147, S.190, D.214 Ligands: GTP.6 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.147, G:S.190

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.5: 12 residues within 4Å: Chain F: R.236, K.517, H.659, K.684, H.685, Y.688, Y.689, N.692, K.697, G.698 Chain R: R.170, K.171 18 PLIP interactions: 4 interactions with chain R, 14 interactions with chain F Salt bridges: R:R.170, R:R.170, R:R.170, R:K.171, F:R.236, F:K.517, F:K.517, F:K.517, F:H.659, F:H.659, F:K.681, F:K.684, F:H.685, F:K.697 Hydrogen bonds: F:Y.688, F:Y.688, F:Y.689, F:N.692

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

GTP.6: 19 residues within 4Å: Chain G: L.142, H.143, S.144, G.145, K.146, T.147, S.148, R.176, L.189, S.190, P.216, G.217, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.7 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:H.143, G:H.143, G:S.144, G:S.144, G:G.145, G:K.146, G:T.147, G:S.148, G:S.148, G:S.190, G:S.190, G:G.217, G:K.269, G:R.272, G:T.316, G:K.317 Salt bridges: G:H.143, G:K.146, G:K.146, G:D.271 pi-Cation interactions: G:K.269

7 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain J: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.13, J:C.16, J:C.71, J:C.74 ZN.9: 4 residues within 4Å: Chain J: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.34, J:C.37, J:C.61, J:C.64 ZN.10: 4 residues within 4Å: Chain K: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.73, K:C.81, K:C.87, K:H.91 ZN.11: 6 residues within 4Å: Chain M: C.104, C.105, C.108, C.148 Ligands: ZN.12, ZN.13 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.104, M:C.105, M:C.108, M:C.148 ZN.12: 5 residues within 4Å: Chain M: C.104, C.122, C.150, C.153 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.104, M:C.122, M:C.150, M:C.153 ZN.13: 5 residues within 4Å: Chain M: C.108, C.120, C.122, C.145 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.108, M:C.120, M:C.122, M:C.145 ZN.14: 5 residues within 4Å: Chain R: C.122, N.124, C.125, H.130, C.135 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.122, R:C.125, R:H.130, R:C.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Structure of the yeast spliceosomal postcatalytic P complex. Science (2017)

Release Date

2018-02-21

Peptides

Pre-mRNA-splicing factor Prp8: F
Pre-mRNA-splicing factor SNU114: G
Pre-mRNA-splicing factor PRP46: H
Pre-mRNA-processing protein 45: I
Pre-mRNA-splicing factor SLT11: J
Pre-mRNA-splicing factor CWC2: K
Pre-mRNA-splicing factor CWC15: L
Pre-mRNA-splicing factor BUD31: M
Pre-mRNA-splicing factor CWC21: N
Pre-mRNA-splicing factor CWC22: O
Pre-mRNA-processing factor Prp17: P
Pre-mRNA-splicing factor Prp18: Q
Pre-mRNA-splicing factor SLU7: R
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22: S
Pre-mRNA-splicing factor SYF2: T
Pre-mRNA-splicing factor CEF1: U
Pre-mRNA-splicing factor CLF1: V
Pre-mRNA-splicing factor SYF1: W
Unknown protein fragment: X
Unknown protein fragment: Y
Small nuclear ribonucleoprotein Sm D2: Zc
Small nuclear ribonucleoprotein F: 08
Small nuclear ribonucleoprotein E: 17
Small nuclear ribonucleoprotein G: 29
Small nuclear ribonucleoprotein-associated protein B: 36
Small nuclear ribonucleoprotein Sm D3: 4a
Small nuclear ribonucleoprotein Sm D1: 5b
Lea1: d
Msl1: e
Pre-mRNA-processing factor Prp19: fghi
Pre-mRNA-splicing factor SNT309: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

F
A

G
B

H
D

I
E

J
F

K
G

L
H

M
I

N
K

O
L

P
M

Q
N

R
O

S
P

T
R

U
S

V
T

W
U

X
X

Y
Y

Z
a

c
q

0
b

8
m

1
c

7
l

2
d

9
n

3
f

6
k

4
g

a
o

5
h

b
p

d
r

e
s

f
u

g
v

h
w

i
x

j
y

Pre-mRNA-splicing factor Prp8

Pre-mRNA-splicing factor SNU114

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 CWC21

Pre-mRNA-splicing factor CWC22

Pre-mRNA-processing factor Prp17

Pre-mRNA-splicing factor Prp18

Pre-mRNA-splicing factor SLU7

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22

Pre-mRNA-splicing factor SYF2

Pre-mRNA-splicing factor CEF1

Pre-mRNA-splicing factor CLF1

Pre-mRNA-splicing factor SYF1

Unknown protein fragment

Unknown protein fragment

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein-associated protein B

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D1

Lea1

Msl1

Pre-mRNA-processing factor Prp19

Pre-mRNA-splicing factor SNT309

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