SMTL ID : 7w5a.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 11 residues within 4Å: Chain A: R.163, K.442, H.584, K.609, H.610, Y.613, N.617, K.623, G.624 Chain r: K.166, R.167 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain r 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, r:K.166, r:K.166, r:K.166, r:R.167, r:R.167 Hydrogen bonds: r:R.167

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

GTP.2: 21 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:H.139, C:H.140, C:G.141, C:K.142, C:T.143, C:T.143, C:T.143, C:C.144, C:G.180, C:G.207, C:H.208, C:K.259, C:E.266, C:S.311, C:Q.313 Salt bridges: C:H.139, C:H.139, C:K.142, C:D.261

9 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: 4 residues within 4Å: Chain E: G.54, G.72, U.74 Chain F: G.46 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain E: U.52, A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: G.71, G.75 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: Q.675 Chain E: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: A.48, A.50 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain Q: 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)

7 x ZN: ZINC ION(Non-covalent)

ZN.10: 6 residues within 4Å: Chain N: C.105, C.117, C.119, C.134 Ligands: ZN.11, ZN.12 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.105, N:C.117, N:C.134 ZN.11: 6 residues within 4Å: Chain N: C.101, C.102, C.105, C.137 Ligands: ZN.10, ZN.12 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.102, N:C.105, N:C.137 ZN.12: 7 residues within 4Å: Chain N: C.101, C.105, C.119, C.139, C.142 Ligands: ZN.10, ZN.11 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.101, N:C.119, N:C.142 ZN.13: 5 residues within 4Å: Chain O: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.24, O:C.27, O:C.81, O:C.84 ZN.14: 4 residues within 4Å: Chain O: C.45, C.48, C.71, C.74 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.45, O:C.48, O:C.71, O:C.74 ZN.15: 4 residues within 4Å: Chain O: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.165, O:C.173, O:C.179, O:H.183 ZN.19: 5 residues within 4Å: Chain r: C.120, C.123, H.128, K.129, C.133 3 PLIP interactions: 3 interactions with chain r Metal complexes: r:C.120, r:H.128, r:C.133

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

ATP.16: 11 residues within 4Å: Chain Q: 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 Q Hydrogen bonds: Q:Q.801, Q:G.826, Q:G.828, Q:K.829, Q:T.830, Q: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: C
U5 small nuclear ribonucleoprotein 40 kDa protein: D
Pre-mRNA-splicing factor SYF1: I
Crooked neck-like protein 1: J
Pre-mRNA-splicing factor SPF27: K
Cell division cycle 5-like protein: L
Pre-mRNA-splicing factor SYF2: M
Protein BUD31 homolog: N
Pre-mRNA-splicing factor RBM22: O
Spliceosome-associated protein CWC15 homolog: P
RNA helicase aquarius: Q
SNW domain-containing protein 1: R
Peptidyl-prolyl cis-trans isomerase-like 1: S
Pleiotropic regulator 1: T
Serine/arginine repetitive matrix protein 2: U
Pre-mRNA-splicing factor CWC22 homolog: V
Pre-mRNA-processing factor 17: W
PSME3-interacting protein: X
ATP-dependent RNA helicase DHX8: Y
Cactin: Z
PRKR-interacting protein 1: 0
Protein FAM32A: 1
Small nuclear ribonucleoprotein-associated proteins B and B': 2j
Peptidyl-prolyl cis-trans isomerase E: 3
Small nuclear ribonucleoprotein Sm D3: 4i
Small nuclear ribonucleoprotein Sm D1: 5k
Small nuclear ribonucleoprotein Sm D2: 6l
Small nuclear ribonucleoprotein F: 7m
Small nuclear ribonucleoprotein E: 8n
Small nuclear ribonucleoprotein G: 9o
Protein mago nashi homolog: a
RNA-binding protein 8A: b
Eukaryotic initiation factor 4A-III: c
Protein CASC3: d
Pre-mRNA-processing factor 19: efgh
U2 small nuclear ribonucleoprotein A': p
U2 small nuclear ribonucleoprotein B'': q
Pre-mRNA-splicing factor SLU7: r

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
E

I
I

J
J

K
K

L
L

M
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

0
2

1
z

2
b

j
i

3
y

4
a

i
h

5
c

k
j

6
d

l
k

7
f

m
m

8
e

n
l

9
g

o
n

a
v

b
w

c
u

d
x

e
q

f
r

g
s

h
t

p
o

q
p

r
1

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

Pre-mRNA-splicing factor SPF27

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

PSME3-interacting protein

ATP-dependent RNA helicase DHX8

Cactin

PRKR-interacting protein 1

Protein FAM32A

Small nuclear ribonucleoprotein-associated proteins B and B'

Peptidyl-prolyl cis-trans isomerase E

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

Pre-mRNA-processing factor 19

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor SLU7

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