SMTL ID : 5z57.1

Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 6.50 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 9 residues within 4Å: Chain A: K.155, K.442, H.584, K.606, K.609, H.610, Y.613, K.623, G.624 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.1546 Salt bridges: A:K.155, 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 ALA: ALANINE(Non-covalent)

ALA.2: 2 residues within 4Å: Chain A: F.166, Q.1552 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.1552 Hydrogen bonds: A:F.166

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

GTP.3: 15 residues within 4Å: Chain A: P.335 Chain C: L.138, H.139, G.141, K.142, T.143, C.144, G.207, K.259, D.261, R.262, E.266, S.311, Q.313 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:H.139, C:G.141, C:K.142, C:T.143, C:T.143, C:C.144, C:G.180, C:G.207 Salt bridges: C:H.139, C:D.261, C:E.266 pi-Cation interactions: C:K.259

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

MG.4: 2 residues within 4Å: Chain C: T.143 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.5: 3 residues within 4Å: Chain M: G.72, U.74 Chain N: G.61 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain M: U.52, A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain M: G.75 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain M: U.74, G.75 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: Q.675 Chain M: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP)

10 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain 0: C.56, C.59, T.61, H.72, H.78 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.56, 0:C.59, 0:H.72, 0:H.78 ZN.11: 5 residues within 4Å: Chain 6: C.23, K.25, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.23, 6:C.26, 6:C.58, 6:C.61 ZN.12: 5 residues within 4Å: Chain 6: C.11, K.13, C.46, C.49, C.85 2 PLIP interactions: 2 interactions with chain 6 Metal complexes: 6:C.46, 6:C.49 ZN.13: 4 residues within 4Å: Chain 6: C.30, C.33, C.72, C.75 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.30, 6:C.33, 6:C.72, 6:C.75 ZN.14: 7 residues within 4Å: Ligands: ZN.15, ZN.16 Chain h: C.105, C.117, C.119, C.134, C.137 4 PLIP interactions: 4 interactions with chain h Metal complexes: h:C.105, h:C.117, h:C.119, h:C.134 ZN.15: 8 residues within 4Å: Ligands: ZN.14, ZN.16 Chain h: C.101, C.102, C.105, C.119, C.137, C.139 4 PLIP interactions: 4 interactions with chain h Metal complexes: h:C.101, h:C.102, h:C.105, h:C.137 ZN.16: 7 residues within 4Å: Ligands: ZN.14, ZN.15 Chain h: C.101, C.105, C.119, C.139, C.142 4 PLIP interactions: 4 interactions with chain h Metal complexes: h:C.101, h:C.119, h:C.139, h:C.142 ZN.17: 5 residues within 4Å: Chain i: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:C.27, i:C.81, i:T.83, i:C.84 ZN.18: 6 residues within 4Å: Chain i: C.45, I.47, C.48, A.49, C.71, C.74 3 PLIP interactions: 3 interactions with chain i Metal complexes: i:C.45, i:C.48, i:C.74 ZN.19: 6 residues within 4Å: Chain M: A.28 Chain i: C.165, W.168, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:C.165, i:C.173, i:C.179, i:H.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structure of the human activated spliceosome in three conformational states. Cell Res. (2018)

Release Date

2018-09-19

Peptides

Pre-mRNA-processing-splicing factor 8: A
116 kDa U5 small nuclear ribonucleoprotein component: C
U5 small nuclear ribonucleoprotein 200 kDa helicase: D
U5 small nuclear ribonucleoprotein 40 kDa protein: E
Small nuclear ribonucleoprotein Sm D3: FP
Small nuclear ribonucleoprotein-associated proteins B and B': GQ
Small nuclear ribonucleoprotein Sm D1: HR
Small nuclear ribonucleoprotein Sm D2: IS
Small nuclear ribonucleoprotein F: JT
Small nuclear ribonucleoprotein E: KU
Small nuclear ribonucleoprotein G: LV
U2 small nuclear ribonucleoprotein A': W
U2 small nuclear ribonucleoprotein B'': X
Splicing factor 3A subunit 3: Y
Splicing factor 3A subunit 1: Z
Splicing factor 3A subunit 2: 0
Splicing factor 3B subunit 1: 1
Splicing factor 3B subunit 2: 2
Splicing factor 3B subunit 3: 3
Splicing factor 3B subunit 4: 4
Splicing factor 3B subunit 6: 5
PHD finger-like domain-containing protein 5A: 6
Splicing factor 3B subunit 5: 7
Crooked neck-like protein 1: 8
Cell division cycle 5-like protein: 9
Pre-mRNA-processing factor 19: abcd
Pre-mRNA-splicing factor SPF27: e
Pre-mRNA-splicing factor SYF1: f
Intron-binding protein aquarius: g
Protein BUD31 homolog: h
Pre-mRNA-splicing factor RBM22: i
Spliceosome-associated protein CWC15 homolog: j
Skip: k
Peptidyl-prolyl cis-trans isomerase-like 1: l
Pleiotropic regulator 1: m
Serine/arginine repetitive matrix protein 2: n
Pre-mRNA-splicing factor CWC22 homolog: o
Pre-mRNA-processing factor 17: p
Smad nuclear-interacting protein 1: q
RNA-binding motif protein, X-linked 2: r
BUD13 homolog: s
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: t
Peptidyl-prolyl cis-trans isomerase E: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
E

F
a

P
h

G
b

Q
i

H
c

R
j

I
d

S
k

J
f

T
m

K
e

U
l

L
g

V
n

W
o

X
p

Y
w

Z
u

0
v

1
1

2
2

3
3

4
4

5
5

6
6

7
7

8
J

9
L

a
q

b
r

c
s

d
t

e
K

f
I

g
Q

h
N

i
O

j
P

k
R

l
S

m
T

n
U

o
V

p
W

q
X

r
Y

s
Z

t
x

u
y

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

U5 small nuclear ribonucleoprotein 200 kDa helicase

U5 small nuclear ribonucleoprotein 40 kDa protein

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Splicing factor 3A subunit 3

Splicing factor 3A subunit 1

Splicing factor 3A subunit 2

Splicing factor 3B subunit 1

Splicing factor 3B subunit 2

Splicing factor 3B subunit 3

Splicing factor 3B subunit 4

Splicing factor 3B subunit 6

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 5

Crooked neck-like protein 1

Cell division cycle 5-like protein

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SPF27

Pre-mRNA-splicing factor SYF1

Intron-binding protein aquarius

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Spliceosome-associated protein CWC15 homolog

Skip

Peptidyl-prolyl cis-trans isomerase-like 1

Pleiotropic regulator 1

Serine/arginine repetitive matrix protein 2

Pre-mRNA-splicing factor CWC22 homolog

Pre-mRNA-processing factor 17

Smad nuclear-interacting protein 1

RNA-binding motif protein, X-linked 2

BUD13 homolog

Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16

Peptidyl-prolyl cis-trans isomerase E

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