SMTL ID : 7qtt.1

Structural organization of a late activated human spliceosome (Baqr, core region)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain D: C.11, I.45, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.11, D:C.46, D:C.49, D:C.85 ZN.2: 4 residues within 4Å: Chain D: C.30, C.33, C.72, C.75 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.30, D:C.33, D:C.72, D:C.75 ZN.3: 4 residues within 4Å: Chain D: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.23, D:C.26, D:C.58, D:C.61 ZN.4: 4 residues within 4Å: Chain H: C.56, C.59, H.72, H.78 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.56, H:C.59, H:H.72, H:H.78, H:H.78 ZN.5: 4 residues within 4Å: Chain I: C.408, C.411, H.425, H.431 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.408, I:C.411, I:H.425, I:H.431 ZN.6: 5 residues within 4Å: Chain O: C.105, C.117, C.119, C.134 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.105, O:C.117, O:C.119, O:C.134 ZN.7: 5 residues within 4Å: Chain O: C.101, C.119, C.139, C.142 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.119, O:C.139, O:C.142 ZN.8: 6 residues within 4Å: Chain O: C.101, C.102, C.105, C.137 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.102, O:C.105, O:C.137 ZN.9: 5 residues within 4Å: Chain P: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.24, P:C.27, P:C.81, P:C.84 ZN.10: 4 residues within 4Å: Chain P: C.45, C.48, C.71, C.74 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.45, P:C.48, P:C.71, P:C.74 ZN.11: 4 residues within 4Å: Chain P: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.165, P:C.173, P:C.179, P:H.183 ZN.12: 4 residues within 4Å: Chain U: C.202, C.211, C.217, H.221 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.202, U:C.211, U:C.217, U:H.221

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.13: 9 residues within 4Å: Chain V: R.163, K.442, H.584, K.609, H.610, Y.613, Y.614, K.623, G.624 13 PLIP interactions: 13 interactions with chain V Hydrogen bonds: V:Y.613 Salt bridges: V:R.163, V:K.442, V:K.442, V:K.442, V:H.584, V:H.584, V:K.606, V:K.609, V:K.609, V:K.609, V:H.610, V:K.623

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

GTP.14: 19 residues within 4Å: Chain W: H.139, H.140, G.141, K.142, T.143, C.144, D.164, V.179, G.180, P.206, G.207, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.15 21 PLIP interactions: 21 interactions with chain W Hydrogen bonds: W:H.139, W:H.140, W:G.141, W:K.142, W:T.143, W:T.143, W:C.144, W:D.164, W:D.164, W:G.180, W:G.207, W:K.259, W:S.311, W:S.312, W:Q.313, W:Q.313 Salt bridges: W:H.139, W:H.139, W:K.142, W:K.142, W:D.261

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

MG.15: 2 residues within 4Å: Chain W: T.143 Ligands: GTP.14 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:T.143 MG.16: 3 residues within 4Å: Chain X: G.54, G.72, U.74 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain H: K.10 Chain X: A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain X: G.75 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain X: U.74, G.75 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain X: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain X: A.48, A.50 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitzova, J. et al., Structural basis of catalytic activation in human splicing. Nature (2023)

Release Date

2023-05-10

Peptides

Splicing factor 3B subunit 3: A
Splicing factor 3B subunit 5: B
Splicing factor 3B subunit 1: C
PHD finger-like domain-containing protein 5A: D
Splicing factor 3B subunit 2: E
Splicing factor 3B subunit 4: F
G-patch domain and KOW motifs-containing protein: G
Splicing factor 3A subunit 2: H
Splicing factor 3A subunit 3: I
BUD13 homolog: J
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: K
Pleiotropic regulator 1: L
Cell division cycle 5-like protein: M
Spliceosome-associated protein CWC15 homolog: N
Protein BUD31 homolog: O
Pre-mRNA-splicing factor RBM22: P
Peptidyl-prolyl cis-trans isomerase-like 4: Q
Pre-mRNA-splicing factor CWC22 homolog: R
Crooked neck-like protein 1: S
SNW domain-containing protein 1: T
RING finger protein 113A: U
Pre-mRNA-processing-splicing factor 8: V
116 kDa U5 small nuclear ribonucleoprotein component: W
Small nuclear ribonucleoprotein F: 1
Small nuclear ribonucleoprotein E: 2
Small nuclear ribonucleoprotein Sm D3: 3
Small nuclear ribonucleoprotein Sm D1: 4
Small nuclear ribonucleoprotein Sm D2: 5
Small nuclear ribonucleoprotein G: 6
Small nuclear ribonucleoprotein-associated proteins B and B': 7
Peptidyl-prolyl cis-trans isomerase-like 1: 8
Serine/arginine repetitive matrix protein 2: 9
RING-type E3 ubiquitin-protein ligase PPIL2: a

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
I

I
J

J
L

K
N

L
O

M
P

N
Q

O
T

P
U

Q
V

R
W

S
X

T
Y

U
Z

V
a

W
b

1
h

2
i

3
j

4
k

5
l

6
m

7
n

8
p

9
q

a
u

Splicing factor 3B subunit 3

Splicing factor 3B subunit 5

Splicing factor 3B subunit 1

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 2

Splicing factor 3B subunit 4

G-patch domain and KOW motifs-containing protein

Splicing factor 3A subunit 2

Splicing factor 3A subunit 3

BUD13 homolog

Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16

Pleiotropic regulator 1

Cell division cycle 5-like protein

Spliceosome-associated protein CWC15 homolog

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Peptidyl-prolyl cis-trans isomerase-like 4

Pre-mRNA-splicing factor CWC22 homolog

Crooked neck-like protein 1

SNW domain-containing protein 1

RING finger protein 113A

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein-associated proteins B and B'

Peptidyl-prolyl cis-trans isomerase-like 1

Serine/arginine repetitive matrix protein 2

RING-type E3 ubiquitin-protein ligase PPIL2

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