SMTL ID : 8h6l.1

Cryo-EM structure of human exon-defined spliceosome in the early B state.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-3-3-3-3-3-3-3-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain C: R.163, K.442, Y.580, H.584, K.606, K.609, H.610, Y.613, Y.614, K.623 9 PLIP interactions: 9 interactions with chain C Salt bridges: C:R.163, C:K.442, C:K.442, C:K.442, C:H.584, C:K.606, C:K.609, C:K.609, C:K.609

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

GTP.2: 18 residues within 4Å: Chain D: L.138, H.139, H.140, G.141, K.142, T.143, C.144, V.179, G.180, P.206, G.207, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:H.139, D:H.139, D:G.141, D:K.142, D:T.143, D:C.144, D:G.180, D:G.207, D:K.259, D:S.312, D:Q.313 Salt bridges: D:H.139, D:K.142, D:K.142, D:D.261

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain D: T.143, D.204 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.143

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain 3: C.13, C.16, H.30, H.36 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:C.13, 3:C.16, 3:H.30, 3:H.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Structural insights into human exon-defined spliceosome prior to activation. Cell Res. (2024)

Release Date

2024-05-01

Peptides

Pre-mRNA-processing-splicing factor 8: C
116 kDa U5 small nuclear ribonucleoprotein component: D
U5 small nuclear ribonucleoprotein 200 kDa helicase: E
U5 small nuclear ribonucleoprotein 40 kDa protein: F
Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B': G6q
Small nuclear ribonucleoprotein Sm D1: H7r
Small nuclear ribonucleoprotein Sm D2: I8s
Small nuclear ribonucleoprotein F: J9t
Small nuclear ribonucleoprotein E: Kau
Small nuclear ribonucleoprotein G: Lbv
Small nuclear ribonucleoprotein Sm D3: Mcw
U6 snRNA-associated Sm-like protein LSm2: O
U6 snRNA-associated Sm-like protein LSm3: P
U6 snRNA-associated Sm-like protein LSm4: Q
U6 snRNA-associated Sm-like protein LSm5: R
U6 snRNA-associated Sm-like protein LSm6: S
U6 snRNA-associated Sm-like protein LSm7: T
U6 snRNA-associated Sm-like protein LSm8: U
U4/U6 small nuclear ribonucleoprotein Prp3: W
U4/U6 small nuclear ribonucleoprotein Prp4: X
U4/U6 small nuclear ribonucleoprotein Prp31: Y
NHP2-like protein 1: Z
Thioredoxin-like protein 4A: 0
Pre-mRNA-processing factor 6: 1
Peptidyl-prolyl cis-trans isomerase H: 2
WW domain-binding protein 4: 3
U4/U6.U5 tri-snRNP-associated protein 1: 4
WD40 repeat-containing protein SMU1: 5
U2 small nuclear ribonucleoprotein A': e
U2 small nuclear ribonucleoprotein B'': f
Splicing factor 3A subunit 1: g
Splicing factor 3A subunit 2: h
Splicing factor 3A subunit 3: i
Splicing factor 3B subunit 1: j
Splicing factor 3B subunit 2: k
Splicing factor 3B subunit 3: l
Splicing factor 3B subunit 4: m
Splicing factor 3B subunit 6: n
PHD finger-like domain-containing protein 5A: o
Splicing factor 3B subunit 5: p

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
5B

D
5C

E
5D

F
5E

G
5a

6
4a

q
2a

H
5b

7
4b

r
2b

I
5c

8
4c

s
2c

J
5d

9
4d

t
2d

K
5e

a
4e

u
2e

L
5f

b
4f

v
2f

M
5g

c
4g

w
2g

O
6a

P
6b

Q
6c

R
6d

S
6e

T
6f

U
6g

W
4B

X
4C

Y
4D

Z
4E

0
4F

1
4G

2
4H

3
4I

4
4J

5
4Z

e
2B

f
2C

g
2D

h
2E

i
2F

j
2G

k
2H

l
2I

m
2J

n
2K

o
2L

p
2M

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

Isoform SM-B of 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

Small nuclear ribonucleoprotein Sm D3

U6 snRNA-associated Sm-like protein LSm2

U6 snRNA-associated Sm-like protein LSm3

U6 snRNA-associated Sm-like protein LSm4

U6 snRNA-associated Sm-like protein LSm5

U6 snRNA-associated Sm-like protein LSm6

U6 snRNA-associated Sm-like protein LSm7

U6 snRNA-associated Sm-like protein LSm8

U4/U6 small nuclear ribonucleoprotein Prp3

U4/U6 small nuclear ribonucleoprotein Prp4

U4/U6 small nuclear ribonucleoprotein Prp31

NHP2-like protein 1

Thioredoxin-like protein 4A

Pre-mRNA-processing factor 6

Peptidyl-prolyl cis-trans isomerase H

WW domain-binding protein 4

U4/U6.U5 tri-snRNP-associated protein 1

WD40 repeat-containing protein SMU1

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Splicing factor 3A subunit 1

Splicing factor 3A subunit 2

Splicing factor 3A subunit 3

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

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