SMTL ID : 7w5b.1

The cryo-EM structure of human C* complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-2-2-2-2-2-2-4-1-1-1-1-1-1-1-1-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 n: K.166, R.167 16 PLIP interactions: 6 interactions with chain n, 10 interactions with chain A Hydrogen bonds: n:R.167 Salt bridges: n:K.166, n:K.166, n:K.166, n:R.167, n:R.167, 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 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 18 PLIP interactions: 18 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: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 F: G.54, G.72, U.74 Chain G: G.46 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain F: U.52, A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain F: G.71, G.75 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: Q.675 Chain F: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain F: A.48, A.50 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain R: 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 O: C.105, C.117, C.119, C.134 Ligands: ZN.11, ZN.12 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:C.105, O:C.117, O:C.134 ZN.11: 6 residues within 4Å: Chain O: C.101, C.102, C.105, C.137 Ligands: ZN.10, ZN.12 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:C.102, O:C.105, O:C.137 ZN.12: 7 residues within 4Å: Chain O: C.101, C.105, C.119, C.139, C.142 Ligands: ZN.10, ZN.11 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:C.101, O:C.119, O:C.142 ZN.13: 5 residues within 4Å: Chain P: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.24, P:C.27, P:C.81, P:C.84 ZN.14: 4 residues within 4Å: Chain P: C.45, C.48, C.71, C.74 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.45, P:C.48, P:C.71, P:C.74 ZN.15: 4 residues within 4Å: Chain P: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.165, P:C.173, P:C.179, P:H.183 ZN.19: 5 residues within 4Å: Chain n: C.120, C.123, H.128, K.129, C.133 3 PLIP interactions: 3 interactions with chain n Metal complexes: n:C.120, n:H.128, n:C.133

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

ATP.16: 11 residues within 4Å: Chain R: 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 R Hydrogen bonds: R:Q.801, R:G.826, R:G.828, R:K.829, R:T.830, R: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 200 kDa helicase: D
U5 small nuclear ribonucleoprotein 40 kDa protein: E
Pre-mRNA-splicing factor SYF1: J
Crooked neck-like protein 1: K
Pre-mRNA-splicing factor SPF27: L
Cell division cycle 5-like protein: M
Pre-mRNA-splicing factor SYF2: N
Protein BUD31 homolog: O
Pre-mRNA-splicing factor RBM22: P
Spliceosome-associated protein CWC15 homolog: Q
RNA helicase aquarius: R
SNW domain-containing protein 1: S
Peptidyl-prolyl cis-trans isomerase-like 1: T
Pleiotropic regulator 1: U
Serine/arginine repetitive matrix protein 2: V
Pre-mRNA-splicing factor CWC22 homolog: W
Pre-mRNA-processing factor 17: 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': 2f
Peptidyl-prolyl cis-trans isomerase E: 3
Small nuclear ribonucleoprotein Sm D3: 4e
Small nuclear ribonucleoprotein Sm D1: 5g
Small nuclear ribonucleoprotein Sm D2: 6h
Small nuclear ribonucleoprotein F: 7i
Small nuclear ribonucleoprotein E: 8j
Small nuclear ribonucleoprotein G: 9k
Pre-mRNA-processing factor 19: abcd
U2 small nuclear ribonucleoprotein A': l
U2 small nuclear ribonucleoprotein B'': m
Pre-mRNA-splicing factor SLU7: n
Protein mago nashi homolog: o
RNA-binding protein 8A: p
Eukaryotic initiation factor 4A-III: q
Protein CASC3: r
NF-kappa-B-activating protein: s

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
E

J
I

K
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
Y

Z
Z

0
2

1
z

2
b

f
i

3
y

4
a

e
h

5
c

g
j

6
d

h
k

7
f

i
m

8
e

j
l

9
g

k
n

a
q

b
r

c
s

d
t

l
o

m
p

n
1

o
v

p
w

q
u

r
x

s
3

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

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

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

Pre-mRNA-processing factor 19

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Pre-mRNA-splicing factor SLU7

Protein mago nashi homolog

RNA-binding protein 8A

Eukaryotic initiation factor 4A-III

Protein CASC3

NF-kappa-B-activating protein

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