SMTL ID : 8i0p.1

The cryo-EM structure of human pre-Bact complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: P.335 Chain C: H.137, H.139, H.140, G.141, K.142, T.143, C.144, V.179, G.180, P.206, G.207, H.208, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:H.139, C:H.140, C:G.141, C:K.142, C:T.143, C:C.144, C:G.207, C:H.208, C:S.312, C:Q.313 Salt bridges: C:H.139, C:K.142, C:K.142, C:D.261 pi-Cation interactions: C:K.259

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain C: K.142, T.143, D.204 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain K: C.28, C.31, H.44, H.50 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.28, K:C.31, K:H.44, K:H.50 ZN.4: 4 residues within 4Å: Chain b: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.23, b:C.26, b:C.58, b:C.61 ZN.5: 4 residues within 4Å: Chain b: C.11, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.11, b:C.46, b:C.49, b:C.85 ZN.6: 6 residues within 4Å: Chain b: C.30, I.32, C.33, D.34, C.72, C.75 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.30, b:C.33, b:C.72, b:C.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, X. et al., Molecular basis for the activation of human spliceosome. Nat Commun (2024)

Release Date

2024-07-31

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
Pre-mRNA-splicing factor SYF1: I
Crooked neck-like protein 1: J
DNA/RNA-binding protein KIN17: K
Cell division cycle 5-like protein: L
Protein BUD31 homolog: M
Pre-mRNA-splicing factor RBM22: N
Spliceosome-associated protein CWC15 homolog: O
RNA helicase aquarius: P
SNW domain-containing protein 1: Q
Pleiotropic regulator 1: R
Smad nuclear-interacting protein 1: S
RNA-binding motif protein, X-linked 2: T
BUD13 homolog: U
Splicing factor 3B subunit 1: V
Splicing factor 3B subunit 3: W
U2 small nuclear ribonucleoprotein A': X
U2 small nuclear ribonucleoprotein B'': Y
Small nuclear ribonucleoprotein Sm D2: Zk
Small nuclear ribonucleoprotein F: 0l
Small nuclear ribonucleoprotein-associated proteins B and B': 1i
Small nuclear ribonucleoprotein Sm D3: 2o
Small nuclear ribonucleoprotein G: 3n
Small nuclear ribonucleoprotein E: 4m
Small nuclear ribonucleoprotein Sm D1: 5j
Splicing factor 3A subunit 3: 6
Splicing factor 3A subunit 1: 7
Splicing factor 3B subunit 2: 8
Splicing factor 3B subunit 4: 9
Splicing factor 3B subunit 6: a
PHD finger-like domain-containing protein 5A: b
Splicing factor 3B subunit 5: c
RING-type E3 ubiquitin-protein ligase PPIL2: d
Serine/arginine repetitive matrix protein 1: e
Peptidyl-prolyl cis-trans isomerase E: f
Splicing factor 3A subunit 2: g
Unknown polymer: h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
E

I
I

J
J

K
K

L
L

M
N

N
O

O
P

P
Q

Q
R

R
T

S
X

T
Y

U
Z

V
1

W
3

X
o

Y
p

Z
h

k
c

0
i

l
d

1
m

i
a

2
l

o
g

3
k

n
f

4
j

m
e

5
n

j
b

6
w

7
u

8
2

9
4

a
6

b
7

c
5

d
9

e
8

f
y

g
v

h
z

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-splicing factor SYF1

Crooked neck-like protein 1

DNA/RNA-binding protein KIN17

Cell division cycle 5-like protein

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

Spliceosome-associated protein CWC15 homolog

RNA helicase aquarius

SNW domain-containing protein 1

Pleiotropic regulator 1

Smad nuclear-interacting protein 1

RNA-binding motif protein, X-linked 2

BUD13 homolog

Splicing factor 3B subunit 1

Splicing factor 3B subunit 3

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein Sm D1

Splicing factor 3A subunit 3

Splicing factor 3A subunit 1

Splicing factor 3B subunit 2

Splicing factor 3B subunit 4

Splicing factor 3B subunit 6

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 5

RING-type E3 ubiquitin-protein ligase PPIL2

Serine/arginine repetitive matrix protein 1

Peptidyl-prolyl cis-trans isomerase E

Splicing factor 3A subunit 2

Unknown polymer

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