SMTL ID : 7w59.1

The cryo-EM structure of human pre-C*-I complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-2-2-2-2-2-2-1-1-1-1-1-1-1-4-1-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, N.617, K.623, G.624 10 PLIP interactions: 10 interactions with chain A Salt bridges: A:R.163, A:K.442, A:K.442, A:K.442, A:H.584, A:K.609, A:K.609, A:K.609, A:H.610, A:K.623

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

GTP.2: 21 residues within 4Å: Chain B: L.138, H.139, H.140, G.141, K.142, T.143, C.144, V.179, G.180, T.205, P.206, G.207, H.208, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:H.139, B:H.140, B:G.141, B:K.142, B:T.143, B:T.143, B:T.143, B:C.144, B:G.180, B:G.207, B:H.208, B:K.259, B:E.266, B:S.311, B:Q.313 Salt bridges: B:H.139, B:H.139, B:K.142, B:D.261

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

MG.3: 3 residues within 4Å: Chain B: T.143, G.180 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.143 MG.10: 4 residues within 4Å: Chain D: G.46 Chain S: G.54, G.72, U.74 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain S: U.52, A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain S: G.75 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain S: G.71, G.75 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: Q.675 Chain S: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain S: A.48, A.50 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain 9: T.830 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain I: C.105, C.117, C.119, C.134 Ligands: ZN.5, ZN.6 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.105, I:C.117, I:C.134 ZN.5: 6 residues within 4Å: Chain I: C.101, C.102, C.105, C.137 Ligands: ZN.4, ZN.6 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.102, I:C.105, I:C.137 ZN.6: 7 residues within 4Å: Chain I: C.101, C.105, C.119, C.139, C.142 Ligands: ZN.4, ZN.5 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.101, I:C.119, I:C.142 ZN.7: 5 residues within 4Å: Chain J: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.24, J:C.27, J:C.81, J:C.84 ZN.8: 4 residues within 4Å: Chain J: C.45, C.48, C.71, C.74 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.45, J:C.48, J:C.71, J:C.74 ZN.9: 4 residues within 4Å: Chain J: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.165, J:C.173, J:C.179, J:H.183

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.16: 11 residues within 4Å: Chain 9: I.800, Q.801, F.802, G.826, T.827, G.828, K.829, T.830, D.831, G.1137 Ligands: MG.17 6 PLIP interactions: 6 interactions with chain 9 Hydrogen bonds: 9:Q.801, 9:G.826, 9:G.828, 9:K.829, 9:T.830, 9:D.831

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, X. et al., Mechanism of exon ligation by human spliceosome. Mol.Cell (2022)

Release Date

2022-06-22

Peptides

Pre-mRNA-processing-splicing factor 8: A
116 kDa U5 small nuclear ribonucleoprotein component: B
U5 small nuclear ribonucleoprotein 40 kDa protein: C
Crooked neck-like protein 1: F
Cell division cycle 5-like protein: G
Pre-mRNA-splicing factor SYF2: H
Protein BUD31 homolog: I
Pre-mRNA-splicing factor RBM22: J
Spliceosome-associated protein CWC15 homolog: K
SNW domain-containing protein 1: L
Peptidyl-prolyl cis-trans isomerase-like 1: M
Pleiotropic regulator 1: N
Serine/arginine repetitive matrix protein 2: O
Pre-mRNA-splicing factor CWC22 homolog: P
Pre-mRNA-processing factor 17: Q
Small nuclear ribonucleoprotein-associated proteins B and B': Ub
PSME3-interacting protein: V
Pre-mRNA-splicing factor SYF1: W
Peptidyl-prolyl cis-trans isomerase E: X
ATP-dependent RNA helicase DHX8: Y
Small nuclear ribonucleoprotein Sm D3: Za
Small nuclear ribonucleoprotein Sm D1: 0c
Small nuclear ribonucleoprotein Sm D2: 1d
Small nuclear ribonucleoprotein F: 2e
Small nuclear ribonucleoprotein E: 3f
Small nuclear ribonucleoprotein G: 4g
Protein mago nashi homolog: 5
RNA-binding protein 8A: 6
Eukaryotic initiation factor 4A-III: 7
Protein CASC3: 8
RNA helicase aquarius: 9
U2 small nuclear ribonucleoprotein A': h
U2 small nuclear ribonucleoprotein B'': i
Pre-mRNA-processing factor 19: jklm
Pre-mRNA-splicing factor SPF27: n

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

F
J

G
L

H
M

I
N

J
O

K
P

L
R

M
S

N
T

O
U

P
V

Q
W

U
b

b
i

V
X

W
I

X
y

Y
Y

Z
a

a
h

0
c

c
j

1
d

d
k

2
f

e
m

3
e

f
l

4
g

g
n

5
v

6
w

7
u

8
x

9
Q

h
o

i
p

j
q

k
r

l
s

m
t

n
K

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

U5 small nuclear ribonucleoprotein 40 kDa protein

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

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

Small nuclear ribonucleoprotein-associated proteins B and B'

PSME3-interacting protein

Pre-mRNA-splicing factor SYF1

Peptidyl-prolyl cis-trans isomerase E

ATP-dependent RNA helicase DHX8

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Protein mago nashi homolog

RNA-binding protein 8A

Eukaryotic initiation factor 4A-III

Protein CASC3

RNA helicase aquarius

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SPF27

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