SMTL ID : 7dvq.1

Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 11 residues within 4Å: Chain A: R.163, K.442, Y.580, H.584, K.606, K.609, H.610, Y.613, Y.614, K.623, G.624 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.624 Salt bridges: A:R.163, 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, A:K.623

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

GTP.2: 20 residues within 4Å: Chain C: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, C.166, V.179, G.180, G.207, H.208, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:H.139, C:H.140, C:G.141, C:K.142, C:T.143, C:T.143, C:C.144, C:D.164, C:G.180, C:G.207, C:H.208, C:K.259, C:E.266, C:S.312, C:Q.313 Water bridges: C:T.143 Salt bridges: C:H.139, C:K.142, C:K.142, C:D.261

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

MG.3: 2 residues within 4Å: Chain C: T.143 Ligands: GTP.2 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.143, H2O.1, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain M: G.26, G.43, U.45 Chain N: A.20, A.21 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain M: A.25, G.26, U.45 Chain N: A.21 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain M: G.42, G.46 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: Q.675 Chain M: G.26, C.27, G.42 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-functional Binders)

K.8: 4 residues within 4Å: Chain M: G.18, A.25, G.26, U.45 No protein-ligand interaction detected (PLIP) K.9: 1 residues within 4Å: Chain M: C.29 No protein-ligand interaction detected (PLIP)

1 x G5J: 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine(Non-covalent)

G5J.10: 14 residues within 4Å: Chain M: U.1 Chain l: H.14, H.15, R.34, A.35, K.37, Y.39, E.44, K.104, D.108, H.118, Y.121 Chain m: N.42, Y.45 11 PLIP interactions: 1 interactions with chain m, 10 interactions with chain l pi-Cation interactions: m:Y.45 Hydrogen bonds: l:A.35, l:A.35, l:Y.39 Salt bridges: l:H.14, l:K.37, l:K.37, l:E.44, l:K.104 pi-Stacking: l:Y.39, l:Y.39

7 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain W: C.44, C.47, H.62, H.68 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.44, W:C.47, W:H.62, W:H.68 ZN.12: 4 residues within 4Å: Chain 2: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.23, 2:C.26, 2:C.58, 2:C.61 ZN.13: 4 residues within 4Å: Chain 2: C.11, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.11, 2:C.46, 2:C.49, 2:C.85 ZN.14: 4 residues within 4Å: Chain 2: C.30, C.33, C.72, C.75 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.30, 2:C.33, 2:C.72, 2:C.75 ZN.15: 4 residues within 4Å: Chain g: C.202, C.211, C.217, H.221 4 PLIP interactions: 4 interactions with chain g Metal complexes: g:C.202, g:C.211, g:C.217, g:H.221 ZN.16: 4 residues within 4Å: Chain k: C.3, C.6, C.83, C.86 4 PLIP interactions: 4 interactions with chain k Metal complexes: k:C.3, k:C.6, k:C.83, k:C.86 ZN.17: 4 residues within 4Å: Chain k: C.58, C.61, C.73, C.76 4 PLIP interactions: 4 interactions with chain k Metal complexes: k:C.58, k:C.61, k:C.73, k:C.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, R. et al., Structure of the activated human minor spliceosome. Science (2021)

Release Date

2021-03-31

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
Sodium channel modifier 1: W
Splicing factor 3B subunit 1: X
Splicing factor 3B subunit 2: Y
Splicing factor 3B subunit 3: Z
Splicing factor 3B subunit 4: 0
Splicing factor 3B subunit 6: 1
PHD finger-like domain-containing protein 5A: 2
Splicing factor 3B subunit 5: 3
Cell division cycle 5-like protein: 4
Crooked neck-like protein 1: 5
Spliceosome-associated protein CWC15 homolog: 6
SNW domain-containing protein 1: 7
Pleiotropic regulator 1: 8
Smad nuclear-interacting protein 1: 9
RNA-binding motif protein, X-linked 2: a
BUD13 homolog: b
RING-type E3 ubiquitin-protein ligase PPIL2: c
Peptidyl-prolyl cis-trans isomerase CWC27 homolog: d
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: e
G-patch domain and KOW motifs-containing protein: f
RING finger protein 113A: g
Serine/arginine repetitive matrix protein 2: h
Pre-mRNA-splicing factor CWC22 homolog: i
Serine/arginine repetitive matrix protein 1: j
Cysteine-rich PDZ-binding protein: k
RNA-binding protein 48: l
Armadillo repeat-containing protein 7: m

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
v

X
1

Y
2

Z
3

0
4

1
5

2
6

3
7

4
L

5
J

6
P

7
R

8
T

9
X

a
Y

b
Z

c
9

d
z

e
x

f
y

g
M

h
U

i
V

j
8

k
0

l
I

m
K

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

Sodium channel modifier 1

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

Cell division cycle 5-like protein

Crooked neck-like protein 1

Spliceosome-associated protein CWC15 homolog

SNW domain-containing protein 1

Pleiotropic regulator 1

Smad nuclear-interacting protein 1

RNA-binding motif protein, X-linked 2

BUD13 homolog

RING-type E3 ubiquitin-protein ligase PPIL2

Peptidyl-prolyl cis-trans isomerase CWC27 homolog

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

G-patch domain and KOW motifs-containing protein

RING finger protein 113A

Serine/arginine repetitive matrix protein 2

Pre-mRNA-splicing factor CWC22 homolog

Serine/arginine repetitive matrix protein 1

Cysteine-rich PDZ-binding protein

RNA-binding protein 48

Armadillo repeat-containing protein 7

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