SMTL ID : 6id1.1

Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.86 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 9 residues within 4Å: Chain A: R.163, K.442, H.584, K.609, H.610, Y.613, N.617, K.623, G.624 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.613, A:N.617 Salt bridges: A:R.163, A:K.442, A:K.442, A:K.442, A:H.584, A:H.584, A:K.606, A:K.609, A:K.609, A:K.609, A:H.610, A:K.623

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

GTP.2: 21 residues within 4Å: Chain A: P.335 Chain C: L.138, H.139, H.140, G.141, K.142, T.143, C.144, Q.163, L.165, G.178, G.180, G.207, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:H.140, C:G.141, C:K.142, C:T.143, C:C.144, C:Q.163, C:Q.163, C:G.178, C:G.180, C:G.207, C:K.259, C:S.312, C:Q.313 Salt bridges: C:K.142, C:K.142, C:D.261 pi-Cation interactions: C:K.259

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

MG.3: 2 residues within 4Å: Chain C: T.143 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.4: 3 residues within 4Å: Chain E: G.54, G.72, U.74 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain E: A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain E: G.71, G.72, U.74, G.75 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: Q.675 Chain E: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: A.47, A.48, A.50 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain I: C.105, C.117, C.119, C.134 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.105, I:C.117, I:C.119, I:C.134 ZN.11: 5 residues within 4Å: Chain I: C.101, C.102, C.105, C.137 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.101, I:C.102, I:C.105, I:C.137 ZN.12: 4 residues within 4Å: Chain I: C.101, C.119, C.139, C.142 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.101, I:C.119, I:C.139, I:C.142 ZN.13: 5 residues within 4Å: Chain J: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.24, J:C.27, J:C.81, J:C.84 ZN.14: 4 residues within 4Å: Chain J: C.45, C.48, C.71, C.74 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.45, J:C.71, J:C.74 ZN.15: 4 residues within 4Å: Chain J: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.165, J:C.173, J:C.179, J:H.183 ZN.16: 5 residues within 4Å: Chain R: C.675, Y.677, C.678, H.718, H.765 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.675, R:C.678, R:H.718, R:H.765

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structures of the human spliceosomes before and after release of the ligated exon. Cell Res. (2019)

Release Date

2019-03-13

Peptides

Pre-mRNA-processing-splicing factor 8: A
116 kDa U5 small nuclear ribonucleoprotein component: C
U5 small nuclear ribonucleoprotein 40 kDa protein: D
Crooked neck-like protein 1: F
Cell division cycle 5-like protein: G
Pre-mRNA-splicing factor SYF2: H
Protein BUD31 homolog: I
Pre-mRNA-splicing factor RBM22: J
Spliceosome-associated protein CWC15 homolog: K
SNW domain-containing protein 1: L
Peptidyl-prolyl cis-trans isomerase-like 1: M
Pleiotropic regulator 1: N
Pre-mRNA-processing factor 17: O
CWF19-like protein 2: R
Small nuclear ribonucleoprotein Sm D3: S7
Small nuclear ribonucleoprotein-associated protein: T8
Small nuclear ribonucleoprotein Sm D1: U9
Small nuclear ribonucleoprotein Sm D2: Va
Small nuclear ribonucleoprotein F: Wb
Small nuclear ribonucleoprotein E: Xc
Small nuclear ribonucleoprotein G: Yd
Pre-mRNA-processing factor 19: Z012
Pre-mRNA-splicing factor SPF27: 3
Pre-mRNA-splicing factor SYF1: 4
RNA helicase aquarius: 5
Peptidyl-prolyl cis-trans isomerase E: 6
U2 small nuclear ribonucleoprotein A': e
U2 small nuclear ribonucleoprotein B'': f
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15: g

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
E

F
J

G
L

H
M

I
N

J
O

K
P

L
R

M
S

N
T

O
W

R
U

S
a

7
h

T
b

8
i

U
c

9
j

V
d

a
k

W
f

b
m

X
e

c
l

Y
g

d
n

Z
q

0
r

1
s

2
t

3
K

4
I

5
Q

6
y

e
o

f
p

g
V

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

U5 small nuclear ribonucleoprotein 40 kDa protein

Crooked neck-like protein 1

Cell division cycle 5-like protein

Pre-mRNA-splicing factor SYF2

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Spliceosome-associated protein CWC15 homolog

SNW domain-containing protein 1

Peptidyl-prolyl cis-trans isomerase-like 1

Pleiotropic regulator 1

Pre-mRNA-processing factor 17

CWF19-like protein 2

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated protein

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SPF27

Pre-mRNA-splicing factor SYF1

RNA helicase aquarius

Peptidyl-prolyl cis-trans isomerase E

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15

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