SMTL ID : 8i0t.1

The cryo-EM structure of human Bact-III complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-2-2-2-1-4-1-mer

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 9 residues within 4Å: Chain A: K.442, H.584, Q.587, K.606, K.609, H.610, Y.613, Y.614, V.1547 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.587, A:Y.614 Salt bridges: A:K.442, 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:K.609, A:H.610

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

GTP.2: 17 residues within 4Å: Chain C: H.139, H.140, G.141, K.142, T.143, C.144, G.180, T.205, P.206, G.207, K.259, D.261, S.311, S.312, Q.313, Y.314 Ligands: MG.3 16 PLIP interactions: 16 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:G.180, C:G.207, C:K.259, C:S.312, C:Q.313, C:Y.314 Salt bridges: C:K.142, C:K.142, C:D.261

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

MG.3: 2 residues within 4Å: Chain C: T.143 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.4: 5 residues within 4Å: Chain F: G.54, G.72, U.74 Chain G: G.46 Ligands: MG.5 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain F: A.53, G.54, U.74 Ligands: MG.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain F: C.55, G.71 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain F: A.50 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain K: C.202, C.211, C.217, H.221 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.202, K:C.211, K:C.217, K:H.221 ZN.11: 6 residues within 4Å: Chain M: C.105, C.117, C.119, C.134, H.136 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.105, M:C.117, M:C.134 ZN.12: 6 residues within 4Å: Chain M: C.101, C.102, C.105, C.134, C.137 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.102, M:C.105, M:C.134 ZN.13: 4 residues within 4Å: Chain M: C.101, C.119, C.139, C.142 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.101, M:C.119, M:C.139, M:C.142 ZN.14: 4 residues within 4Å: Chain 5: C.23, C.26, C.58, C.61 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:C.23, 5:C.26, 5:C.58 ZN.15: 6 residues within 4Å: Chain 5: C.11, K.13, C.46, E.48, C.49, C.85 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.11, 5:C.46, 5:E.48, 5:C.49 ZN.16: 5 residues within 4Å: Chain 5: C.30, V.31, I.32, C.33, C.75 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:C.30

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
RING finger protein 113A: 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
Peptidyl-prolyl cis-trans isomerase-like 1: R
Pleiotropic regulator 1: S
Serine/arginine repetitive matrix protein 2: T
Pre-mRNA-splicing factor CWC22 homolog: U
Pre-mRNA-processing factor 17: V
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: W
Peptidyl-prolyl cis-trans isomerase-like 4: X
Pre-mRNA-splicing factor SPF27: Y
Splicing factor 3B subunit 1: Z
Splicing factor 3B subunit 3: 0
U2 small nuclear ribonucleoprotein B'': 1
Splicing factor 3A subunit 3: 2
Splicing factor 3B subunit 2: 3
Splicing factor 3B subunit 4: 4
PHD finger-like domain-containing protein 5A: 5
Splicing factor 3B subunit 5: 6
Peptidyl-prolyl cis-trans isomerase E: 7
Splicing factor 3A subunit 2: 8
U2 small nuclear ribonucleoprotein A': 9
Small nuclear ribonucleoprotein Sm D2: ak
Small nuclear ribonucleoprotein F: bl
Small nuclear ribonucleoprotein-associated proteins B and B': ci
Small nuclear ribonucleoprotein Sm D3: do
Small nuclear ribonucleoprotein G: en
Small nuclear ribonucleoprotein E: fm
Small nuclear ribonucleoprotein Sm D1: gj
Splicing factor 3A subunit 1: h
Pre-mRNA-processing factor 19: pqrs
RING-type E3 ubiquitin-protein ligase PPIL2: t

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
S

S
T

T
U

U
V

V
W

W
X

X
Y

Y
Z

Z
1

0
3

1
p

2
w

3
2

4
4

5
7

6
5

7
y

8
v

9
o

a
h

k
c

b
i

l
d

c
m

i
a

d
l

o
g

e
k

n
f

f
j

m
e

g
n

j
b

h
u

p
q

q
r

r
s

s
t

t
9

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

RING finger protein 113A

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

Peptidyl-prolyl cis-trans isomerase-like 1

Pleiotropic regulator 1

Serine/arginine repetitive matrix protein 2

Pre-mRNA-splicing factor CWC22 homolog

Pre-mRNA-processing factor 17

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

Peptidyl-prolyl cis-trans isomerase-like 4

Pre-mRNA-splicing factor SPF27

Splicing factor 3B subunit 1

Splicing factor 3B subunit 3

U2 small nuclear ribonucleoprotein B''

Splicing factor 3A subunit 3

Splicing factor 3B subunit 2

Splicing factor 3B subunit 4

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 5

Peptidyl-prolyl cis-trans isomerase E

Splicing factor 3A subunit 2

U2 small nuclear ribonucleoprotein A'

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 1

Pre-mRNA-processing factor 19

RING-type E3 ubiquitin-protein ligase PPIL2

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