SMTL ID : 5z58.1

Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.90 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 6 residues within 4Å: Chain A: K.442, H.584, Q.587, K.606, K.609, K.623 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.587 Salt bridges: A:K.442, A:H.584, A:K.606, A:K.609, A:K.623

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

GTP.2: 16 residues within 4Å: Chain A: P.335, W.406 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.3 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.139, C:G.141, C:K.142, 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.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 M: G.72, U.74 Chain N: G.61 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain M: U.52, A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain M: G.75 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain M: U.74, G.75 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: Q.675 Chain M: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 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.10: 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.11: 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.12: 5 residues within 4Å: Chain N: G.62 Chain a: C.202, C.211, C.217, H.221 3 PLIP interactions: 3 interactions with chain a Metal complexes: a:C.202, a:C.211, a:C.217

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
RING finger protein 113A: a
Spliceosome-associated protein CWC15 homolog: b
Skip: c
Pleiotropic regulator 1: d
Pre-mRNA-splicing factor CWC22 homolog: e
Smad nuclear-interacting protein 1: f
RNA-binding motif protein, X-linked 2: g
BUD13 homolog: h
Peptidyl-prolyl cis-trans isomerase CWC27 homolog: i
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: j

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
M

b
P

c
R

d
T

e
V

f
X

g
Y

h
Z

i
z

j
x

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

RING finger protein 113A

Spliceosome-associated protein CWC15 homolog

Skip

Pleiotropic regulator 1

Pre-mRNA-splicing factor CWC22 homolog

Smad nuclear-interacting protein 1

RNA-binding motif protein, X-linked 2

BUD13 homolog

Peptidyl-prolyl cis-trans isomerase CWC27 homolog

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

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