SMTL ID : 8y6o.1

Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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-mer

Ligands

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

MG.1: 2 residues within 4Å: Chain B: A.19, A.21 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain D: T.143, D.204 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.143

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 13 residues within 4Å: Chain C: R.163, K.442, Y.580, H.584, K.606, K.609, H.610, Y.613, Y.614, N.617, K.623, G.624 Chain I: E.275 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain I Hydrogen bonds: C:Y.613, C:Y.614, C:N.617, C:G.624, I:E.275 Salt bridges: C:R.163, C:K.442, C:K.442, C:K.442, C:H.584, C:H.584, C:K.606, C:K.606, C:K.609, C:K.609, C:K.609, C:H.610, C:K.623, C:K.623

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

GTP.3: 21 residues within 4Å: Chain D: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, C.166, V.179, G.180, P.206, G.207, H.208, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:H.139, D:H.140, D:G.141, D:K.142, D:T.143, D:C.144, D:D.164, D:G.178, D:G.180, D:G.207, D:H.208, D:K.259, D:Q.313 Salt bridges: D:H.139, D:K.142, D:K.142, D:D.261

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain W: C.7, C.10, H.20, H.26, Q.29 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.7, W:C.10, W:H.20, W:H.26 ZN.6: 4 residues within 4Å: Chain W: C.66, C.69, H.92, H.98 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.66, W:C.69, W:H.92, W:H.98 ZN.7: 5 residues within 4Å: Chain 5: C.57, K.59, C.66, C.72, H.76 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.57, 5:C.66, 5:C.72, 5:H.76 ZN.8: 4 residues within 4Å: Chain 5: C.7, C.10, H.24, H.30 5 PLIP interactions: 5 interactions with chain 5 Metal complexes: 5:C.7, 5:C.10, 5:H.24, 5:H.30, 5:H.30 ZN.9: 4 residues within 4Å: Chain 8: C.58, H.64, H.74, C.78 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.58, 8:H.64, 8:H.74, 8:C.78 ZN.10: 4 residues within 4Å: Chain i: C.136, C.139, H.155, H.161 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:C.136, i:C.139, i:H.155, i:H.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, R. et al., Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science (2024)

Release Date

2024-03-20

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
Pre-mRNA-processing factor 6: G
Thioredoxin-like protein 4B: H
Probable ATP-dependent RNA helicase DDX23: I
Small nuclear ribonucleoprotein-associated proteins B and B': JXa
Small nuclear ribonucleoprotein Sm D1: KYb
Small nuclear ribonucleoprotein Sm D2: LZc
Small nuclear ribonucleoprotein Sm D3: M0d
Small nuclear ribonucleoprotein E: N1e
Small nuclear ribonucleoprotein F: O2f
Small nuclear ribonucleoprotein G: P3g
U4/U6 small nuclear ribonucleoprotein Prp31: S
U4/U6 small nuclear ribonucleoprotein Prp4: T
U4/U6 small nuclear ribonucleoprotein Prp3: U
NHP2-like protein 1: V
Centrosomal AT-AC splicing factor: W
Zinc finger matrin-type protein 5: 5
U11/U12 small nuclear ribonucleoprotein 35 kDa protein: 6
U11/U12 small nuclear ribonucleoprotein 25 kDa protein: 7
U11/U12 small nuclear ribonucleoprotein 48 kDa protein: 8
Programmed cell death protein 7: 9
U4/U6.U5 tri-snRNP-associated protein 1: h
U4/U6.U5 tri-snRNP-associated protein 2: i
Serine/threonine-protein kinase PRP4 homolog: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
a

X
h

a
o

K
b

Y
i

b
p

L
c

Z
j

c
q

M
d

0
k

d
r

N
e

1
l

e
s

O
f

2
m

f
t

P
g

3
n

g
u

S
L

T
M

U
N

V
O

W
R

5
V

6
W

7
X

8
Y

9
Z

h
S

i
U

j
Q

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

Pre-mRNA-processing factor 6

Thioredoxin-like protein 4B

Probable ATP-dependent RNA helicase DDX23

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

U4/U6 small nuclear ribonucleoprotein Prp31

U4/U6 small nuclear ribonucleoprotein Prp4

U4/U6 small nuclear ribonucleoprotein Prp3

NHP2-like protein 1

Centrosomal AT-AC splicing factor

Zinc finger matrin-type protein 5

U11/U12 small nuclear ribonucleoprotein 35 kDa protein

U11/U12 small nuclear ribonucleoprotein 25 kDa protein

U11/U12 small nuclear ribonucleoprotein 48 kDa protein

Programmed cell death protein 7

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

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

Serine/threonine-protein kinase PRP4 homolog

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