SMTL ID : 5mps.1

Structure of a spliceosome remodeled for exon ligation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.85 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-mer

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain B: G.20 Chain D: G.78, A.79, U.80 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain D: A.59, G.60, A.79, U.80 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain D: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP)

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

K.4: 2 residues within 4Å: Chain D: A.62, G.81 No protein-ligand interaction detected (PLIP) K.5: 1 residues within 4Å: Chain D: G.81 No protein-ligand interaction detected (PLIP)

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.6: 11 residues within 4Å: Chain F: R.236, K.517, H.659, K.684, H.685, Y.688, Y.689, K.697, G.698, N.1618 Chain T: R.170 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain T Hydrogen bonds: F:Y.689 Salt bridges: F:R.236, F:K.517, F:K.517, F:H.659, F:H.659, F:K.684, F:H.685, F:K.697, T:R.170, T:R.170, T:R.170

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

GTP.7: 21 residues within 4Å: Chain F: N.405 Chain G: P.141, L.142, H.143, S.144, G.145, K.146, T.147, S.148, R.176, L.189, S.190, A.215, G.217, H.218, K.269, D.271, R.272, S.315, T.316, K.317 23 PLIP interactions: 23 interactions with chain G Hydrogen bonds: G:H.143, G:S.144, G:G.145, G:K.146, G:T.147, G:T.147, G:T.147, G:S.148, G:S.190, G:S.190, G:A.215, G:G.217, G:H.218, G:K.269, G:R.272, G:T.316, G:T.316, G:K.317 Salt bridges: G:H.143, G:H.143, G:K.146, G:K.146 pi-Cation interactions: G:K.269

6 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain K: C.104, C.105, C.108, C.148 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.104, K:C.105, K:C.108, K:C.148 ZN.9: 7 residues within 4Å: Chain K: C.104, C.108, C.122, C.150, C.153 Ligands: ZN.8, ZN.10 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.104, K:C.122, K:C.150, K:C.153 ZN.10: 8 residues within 4Å: Chain K: C.108, C.120, C.122, C.145, C.148, C.150 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.108, K:C.120, K:C.122, K:C.145 ZN.11: 4 residues within 4Å: Chain L: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.73, L:C.81, L:C.87, L:H.91 ZN.12: 4 residues within 4Å: Chain M: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.34, M:C.37, M:C.61, M:C.64 ZN.13: 5 residues within 4Å: Chain M: I.12, C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.13, M:C.16, M:C.71, M:C.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fica, S.M. et al., Structure of a spliceosome remodelled for exon ligation. Nature (2017)

Release Date

2017-01-18

Peptides

Pre-mRNA-splicing factor 8: F
Pre-mRNA-splicing factor SNU114: G
Pre-mRNA-splicing factor CWC22: H
Pre-mRNA-splicing factor PRP46: I
Pre-mRNA-processing protein 45: J
Pre-mRNA-splicing factor BUD31: K
Pre-mRNA-splicing factor CWC2: L
Pre-mRNA-splicing factor SLT11: M
Pre-mRNA-splicing factor CEF1: N
Pre-mRNA-splicing factor CWC15: O
Pre-mRNA-splicing factor CWC21: P
Pre-mRNA-splicing factor CLF1: Q
Pre-mRNA-splicing factor SYF1: R
Pre-mRNA-splicing factor 18: S
Pre-mRNA-splicing factor SLU7: T
Pre-mRNA-processing factor 17: U
Unknown: V
Pre-mRNA-splicing factor SYF2: W
Small nuclear ribonucleoprotein-associated protein B: X
Small nuclear ribonucleoprotein Sm D3: Y
Small nuclear ribonucleoprotein E: Z
Small nuclear ribonucleoprotein F: 0
Small nuclear ribonucleoprotein G: 1
Small nuclear ribonucleoprotein Sm D1: 2
Small nuclear ribonucleoprotein Sm D2: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

F
A

G
C

H
H

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
R

Q
S

R
T

S
a

T
c

U
o

V
X

W
y

X
b

Y
d

Z
e

0
f

1
g

2
h

3
j

Pre-mRNA-splicing factor 8

Pre-mRNA-splicing factor SNU114

Pre-mRNA-splicing factor CWC22

Pre-mRNA-splicing factor PRP46

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor BUD31

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor SLT11

Pre-mRNA-splicing factor CEF1

Pre-mRNA-splicing factor CWC15

Pre-mRNA-splicing factor CWC21

Pre-mRNA-splicing factor CLF1

Pre-mRNA-splicing factor SYF1

Pre-mRNA-splicing factor 18

Pre-mRNA-splicing factor SLU7

Pre-mRNA-processing factor 17

Unknown

Pre-mRNA-splicing factor SYF2

Small nuclear ribonucleoprotein-associated protein B

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

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