SMTL ID : 8h6e.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 11 residues within 4Å: Chain K: R.163, K.442, H.584, K.606, K.609, H.610, Y.613, Y.614, N.617, K.623, G.624 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:Y.613, K:N.617, K:G.624 Salt bridges: K:R.163, K:K.442, K:K.442, K:K.442, K:H.584, K:H.584, K:K.606, K:K.609, K:K.609, K:K.609, K:H.610, K:K.623

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain L: T.143, D.169, D.204 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.143

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

GTP.3: 21 residues within 4Å: Chain L: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, G.178, V.179, G.180, G.207, H.208, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain L Hydrogen bonds: L:H.139, L:H.140, L:G.141, L:G.141, L:K.142, L:T.143, L:C.144, L:D.164, L:G.180, L:G.207, L:H.208, L:K.259, L:S.312, L:Q.313 Salt bridges: L:H.139, L:K.142, L:K.142, L:D.261

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain 4: C.136, C.139, H.155, H.161 3 PLIP interactions: 3 interactions with chain 4 Metal complexes: 4:C.139, 4:H.155, 4:H.161

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

U6 snRNA-associated Sm-like protein LSm2: C
U6 snRNA-associated Sm-like protein LSm3: D
U6 snRNA-associated Sm-like protein LSm4: E
U6 snRNA-associated Sm-like protein LSm5: F
U6 snRNA-associated Sm-like protein LSm6: G
U6 snRNA-associated Sm-like protein LSm7: H
U6 snRNA-associated Sm-like protein LSm8: I
Pre-mRNA-processing-splicing factor 8: K
116 kDa U5 small nuclear ribonucleoprotein component: L
U5 small nuclear ribonucleoprotein 200 kDa helicase: M
U5 small nuclear ribonucleoprotein 40 kDa protein: N
Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B': O8s
Small nuclear ribonucleoprotein Sm D1: P9t
Small nuclear ribonucleoprotein Sm D2: Qau
Small nuclear ribonucleoprotein F: Rbv
Small nuclear ribonucleoprotein E: Scw
Small nuclear ribonucleoprotein G: Tdx
Small nuclear ribonucleoprotein Sm D3: Uey
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
RNA-binding protein 42: 2
U4/U6.U5 tri-snRNP-associated protein 1: 3
U4/U6.U5 tri-snRNP-associated protein 2: 4
Probable ATP-dependent RNA helicase DDX23: 5
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein: 6
Serine/threonine-protein kinase PRP4 homolog: 7
U2 small nuclear ribonucleoprotein A': g
U2 small nuclear ribonucleoprotein B'': h
Splicing factor 3A subunit 1: i
Splicing factor 3A subunit 2: j
Splicing factor 3A subunit 3: k
Splicing factor 3B subunit 1: l
Splicing factor 3B subunit 2: m
Splicing factor 3B subunit 3: n
Splicing factor 3B subunit 4: o
Splicing factor 3B subunit 6: p
PHD finger-like domain-containing protein 5A: q
Splicing factor 3B subunit 5: r

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
6a

D
6b

E
6c

F
6d

G
6e

H
6f

I
6g

K
5B

L
5C

M
5D

N
5E

O
5a

8
4a

s
2a

P
5b

9
4b

t
2b

Q
5c

a
4c

u
2c

R
5d

b
4d

v
2d

S
5e

c
4e

w
2e

T
5f

d
4f

x
2f

U
5g

e
4g

y
2g

W
4B

X
4C

Y
4D

Z
4E

0
4F

1
4G

2
4R

3
4S

4
4T

5
4U

6
4X

7
4Y

g
2B

h
2C

i
2D

j
2E

k
2F

l
2G

m
2H

n
2I

o
2J

p
2K

q
2L

r
2M

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

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

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

RNA-binding protein 42

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

U4/U6.U5 tri-snRNP-associated protein 2

Probable ATP-dependent RNA helicase DDX23

U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein

Serine/threonine-protein kinase PRP4 homolog

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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