SMTL ID : 8i0v.1

The cryo-EM structure of human post-Bact complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 9 residues within 4Å: Chain A: R.163, K.442, H.584, K.609, H.610, Y.613, Y.614, K.623, G.624 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.613, A:Y.614, A:Y.614 Salt bridges: A:R.163, A:K.442, A:K.442, A:K.442, A:H.584, A:H.584, A:K.609, 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: 19 residues within 4Å: Chain C: L.138, H.139, H.140, G.141, K.142, T.143, C.144, V.179, G.180, P.206, G.207, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:H.139, C:G.141, C:G.141, C:K.142, C:T.143, C:C.144, C:G.180, C:G.207, C:S.312, C:Q.313 Salt bridges: C:H.139, C:K.142, C:K.142, C:D.261

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

MG.3: 3 residues within 4Å: Chain C: T.143, G.180 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.4: 6 residues within 4Å: Chain E: G.54, G.72, U.74 Chain F: G.46, G.47 Ligands: MG.5 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain E: A.53, G.54, U.74 Ligands: MG.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain E: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: A.47, U.52 Chain J: K.165 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.10: 6 residues within 4Å: Chain L: C.105, C.117, C.119, C.134, H.136 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.105, L:C.117, L:C.134 ZN.11: 7 residues within 4Å: Chain L: C.101, C.102, C.105, C.134, C.137 Ligands: ZN.10, ZN.12 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.101, L:C.102, L:C.105 ZN.12: 5 residues within 4Å: Chain L: C.101, C.119, C.139, C.142 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.101, L:C.119, L:C.139, L:C.142 ZN.13: 4 residues within 4Å: Chain e: C.23, C.26, C.58, C.61 3 PLIP interactions: 3 interactions with chain e Metal complexes: e:C.23, e:C.26, e:C.58 ZN.14: 4 residues within 4Å: Chain e: C.11, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain e Metal complexes: e:C.11, e:C.46, e:C.49, e:C.85 ZN.15: 6 residues within 4Å: Chain e: C.30, I.32, C.33, C.72, E.74, C.75 3 PLIP interactions: 3 interactions with chain e Metal complexes: e:C.30, e:C.72, e: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 40 kDa protein: D
Pre-mRNA-splicing factor SYF1: H
Crooked neck-like protein 1: I
Cell division cycle 5-like protein: J
Pre-mRNA-splicing factor SYF2: K
Protein BUD31 homolog: L
Pre-mRNA-splicing factor RBM22: M
Spliceosome-associated protein CWC15 homolog: N
RNA helicase aquarius: O
SNW domain-containing protein 1: P
Peptidyl-prolyl cis-trans isomerase-like 1: Q
Pleiotropic regulator 1: R
Serine/arginine repetitive matrix protein 2: S
Pre-mRNA-splicing factor CWC22 homolog: T
Pre-mRNA-processing factor 17: U
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: V
Peptidyl-prolyl cis-trans isomerase-like 4: W
Pre-mRNA-splicing factor SPF27: X
Small nuclear ribonucleoprotein-associated proteins B and B': Yk
Small nuclear ribonucleoprotein Sm D1: Zo
Small nuclear ribonucleoprotein Sm D2: 0i
Small nuclear ribonucleoprotein F: 1j
Small nuclear ribonucleoprotein E: 2n
Small nuclear ribonucleoprotein G: 3m
Small nuclear ribonucleoprotein Sm D3: 4l
Pre-mRNA-processing factor 19: 5678
Peptidyl-prolyl cis-trans isomerase E: 9
Splicing factor 3B subunit 1: a
Splicing factor 3B subunit 3: b
Splicing factor 3B subunit 2: c
Splicing factor 3B subunit 4: d
PHD finger-like domain-containing protein 5A: e
Splicing factor 3B subunit 5: f
U2 small nuclear ribonucleoprotein B'': g
U2 small nuclear ribonucleoprotein A': h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
E

H
I

I
J

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

T
V

U
W

V
X

W
Y

X
Z

Y
a

k
m

Z
b

o
n

0
c

i
h

1
d

j
i

2
e

n
j

3
f

m
k

4
g

l
l

5
q

6
r

7
s

8
t

9
y

a
1

b
3

c
2

d
4

e
7

f
5

g
p

h
o

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

U5 small nuclear ribonucleoprotein 40 kDa protein

Pre-mRNA-splicing factor SYF1

Crooked neck-like protein 1

Cell division cycle 5-like protein

Pre-mRNA-splicing factor SYF2

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

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

Small nuclear ribonucleoprotein Sm D3

Pre-mRNA-processing factor 19

Peptidyl-prolyl cis-trans isomerase E

Splicing factor 3B subunit 1

Splicing factor 3B subunit 3

Splicing factor 3B subunit 2

Splicing factor 3B subunit 4

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 5

U2 small nuclear ribonucleoprotein B''

U2 small nuclear ribonucleoprotein A'

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