SMTL ID : 8i0w.1

The cryo-EM structure of human C complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 12 residues within 4Å: Chain A: R.163, K.442, H.584, K.609, H.610, Y.613, N.617, K.623, G.624, N.1546 Chain n: R.255, K.258 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain n Hydrogen bonds: A:N.617, A:N.1546 Salt bridges: A:R.163, 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:H.610, A:K.623, n:R.255, n:K.258

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, H.208, 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:H.140, C:G.141, C:K.142, C:T.143, C:T.143, C:C.144, C:G.180, C:G.207, C:H.208, C:Q.313 Salt bridges: C:H.139, C:K.142, C:D.261

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

MG.3: 3 residues within 4Å: Chain C: T.143, D.204 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.4: 3 residues within 4Å: Chain F: G.72, U.74 Chain H: G.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: Q.675 Chain F: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain O: C.105, C.117, C.119, C.134, C.137 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.105, O:C.117, O:C.119, O:C.134 ZN.9: 8 residues within 4Å: Chain O: C.101, C.102, C.105, C.119, C.137, C.139 Ligands: ZN.8, ZN.10 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:C.102, O:C.105, O:C.137 ZN.10: 5 residues within 4Å: Chain O: C.101, C.119, C.139, C.142 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.119, O:C.139, O:C.142 ZN.11: 6 residues within 4Å: Chain P: C.24, C.27, C.81, T.83, C.84, R.159 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.24, P:C.27, P:C.81, P:C.84 ZN.12: 5 residues within 4Å: Chain P: C.45, C.48, C.71, T.73, 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.13: 5 residues within 4Å: Chain P: C.165, W.168, 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.14: 5 residues within 4Å: Chain Z: C.43, T.45, C.46, C.80, C.83 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.43, Z:C.46, Z:C.80, Z:C.83

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: 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
SNW domain-containing protein 1: R
Peptidyl-prolyl cis-trans isomerase-like 1: S
Pleiotropic regulator 1: T
RNA helicase aquarius: U
Serine/arginine repetitive matrix protein 2: V
Pre-mRNA-splicing factor CWC22 homolog: W
Pre-mRNA-processing factor 17: X
Pre-mRNA-splicing factor CWC25 homolog: Y
Coiled-coil domain-containing protein 94: Z
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16: 0
Pre-mRNA-processing factor 19: 1234
Eukaryotic initiation factor 4A-III: 5
Protein mago nashi homolog: 6
RNA-binding protein 8A: 7
Protein CASC3: 8
Small nuclear ribonucleoprotein Sm D3: 9v
Small nuclear ribonucleoprotein-associated proteins B and B': ap
Small nuclear ribonucleoprotein Sm D1: bq
Small nuclear ribonucleoprotein Sm D2: cr
Small nuclear ribonucleoprotein F: ds
Small nuclear ribonucleoprotein E: et
Small nuclear ribonucleoprotein G: fu
U2 small nuclear ribonucleoprotein A': g
U2 small nuclear ribonucleoprotein B'': h
Peptidyl-prolyl cis-trans isomerase E: i
Pre-mRNA-splicing factor ISY1 homolog: j
Peptidylprolyl isomerase domain and WD repeat-containing protein 1: k
Corepressor interacting with RBPJ 1: l
WD repeat-containing protein 70: m
Protein FRG1: n
UNK: o

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
R

S
S

T
T

U
Q

V
U

W
V

X
W

Y
X

Z
Y

0
Z

1
q

2
r

3
s

4
t

5
u

6
v

7
w

8
x

9
h

v
g

a
i

p
a

b
j

q
b

c
k

r
c

d
m

s
d

e
l

t
e

f
n

u
f

g
o

h
p

i
y

j
z

k
3

l
4

m
1

n
2

o
5

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

SNW domain-containing protein 1

Peptidyl-prolyl cis-trans isomerase-like 1

Pleiotropic regulator 1

RNA helicase aquarius

Serine/arginine repetitive matrix protein 2

Pre-mRNA-splicing factor CWC22 homolog

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor CWC25 homolog

Coiled-coil domain-containing protein 94

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

Pre-mRNA-processing factor 19

Eukaryotic initiation factor 4A-III

Protein mago nashi homolog

RNA-binding protein 8A

Protein CASC3

Small nuclear ribonucleoprotein Sm D3

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

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Peptidyl-prolyl cis-trans isomerase E

Pre-mRNA-splicing factor ISY1 homolog

Peptidylprolyl isomerase domain and WD repeat-containing protein 1

Corepressor interacting with RBPJ 1

WD repeat-containing protein 70

Protein FRG1

UNK

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