SMTL ID : 5yzg.1

The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.10 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain A: K.155, R.163, K.442, H.584, K.609, H.610, Y.613, K.623, G.624, N.1546 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.1546 Salt bridges: A:K.155, 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:H.610, A:K.623

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

GTP.2: 19 residues within 4Å: Chain A: P.335 Chain C: L.138, H.139, 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:H.139, 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:D.261

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

MG.3: 2 residues within 4Å: Chain C: T.143 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.143 MG.6: 3 residues within 4Å: Chain F: G.72, U.74 Chain G: G.63 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain F: A.53, G.54, U.74 Chain G: G.63, A.206 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain F: U.74, G.75 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain F: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain 5: T.89, D.187, E.188 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:T.89

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 7 residues within 4Å: Chain D: T.480, N.482, G.506, A.507, G.508, K.509, T.510 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.480, D:N.482, D:G.506, D:G.508, D:K.509, D:T.510 ADP.5: 8 residues within 4Å: Chain D: F.1327, F.1328, T.1352, G.1353, S.1354, G.1355, K.1356, T.1357 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:F.1327, D:N.1329, D:G.1353, D:S.1354, D:G.1355, D:K.1356, D:T.1357

7 x ZN: ZINC ION(Non-covalent)

ZN.11: 7 residues within 4Å: Chain O: C.105, C.117, C.119, C.134, C.137 Ligands: ZN.12, ZN.13 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.105, O:C.117, O:C.119, O:C.134 ZN.12: 7 residues within 4Å: Chain O: C.101, C.102, C.105, C.119, C.137 Ligands: ZN.11, ZN.13 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.102, O:C.105, O:C.137 ZN.13: 7 residues within 4Å: Chain O: C.101, C.105, C.119, C.139, C.142 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.119, O:C.139, O:C.142 ZN.14: 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.15: 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.16: 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.17: 6 residues within 4Å: Chain Z: C.43, T.45, C.46, E.48, 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

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.19: 21 residues within 4Å: Chain 5: F.40, Y.56, F.58, K.60, Q.65, Q.83, S.84, G.85, T.86, G.87, K.88, T.89, A.90, E.188, G.340, D.342, P.344, R.367, R.370, Y.371 Ligands: MG.18 21 PLIP interactions: 21 interactions with chain 5 Hydrogen bonds: 5:Q.65, 5:Q.65, 5:G.85, 5:T.86, 5:G.87, 5:K.88, 5:T.89, 5:T.89, 5:A.90, 5:G.340, 5:D.342 Salt bridges: 5:K.88, 5:K.88, 5:R.367, 5:R.370, 5:R.370, 5:R.370 pi-Stacking: 5:F.58, 5:F.58, 5:Y.371, 5:Y.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, X. et al., Structure of a human catalytic step I spliceosome. Science (2018)

Release Date

2018-08-08

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: I
Crooked neck-like protein 1: J
Pre-mRNA-splicing factor SPF27: K
Cell division cycle 5-like protein: L
Pre-mRNA-splicing factor ISY1 homolog: 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
Intron-binding protein 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 2: 6
RNA-binding protein 8A: 7
Protein CASC3: 8
Small nuclear ribonucleoprotein Sm D3: 9i
Small nuclear ribonucleoprotein-associated proteins B and B': aj
Small nuclear ribonucleoprotein Sm D1: bk
Small nuclear ribonucleoprotein Sm D2: cl
Small nuclear ribonucleoprotein F: dm
Small nuclear ribonucleoprotein E: en
Small nuclear ribonucleoprotein G: fo
U2 small nuclear ribonucleoprotein A': g
U2 small nuclear ribonucleoprotein B'': h
Peptidyl-prolyl cis-trans isomerase E: p
Peptidylprolyl isomerase domain and WD repeat-containing protein 1: q
Peptidyl-prolyl cis-trans isomerase G: r
UNKNOW: s

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
E

I
I

J
J

K
K

L
L

M
y

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

i
a

a
i

j
b

b
j

k
c

c
k

l
d

d
m

m
f

e
l

n
e

f
n

o
g

g
o

h
p

p
1

q
2

r
3

s
4

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 ISY1 homolog

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

Intron-binding protein 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 2

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

Peptidylprolyl isomerase domain and WD repeat-containing protein 1

Peptidyl-prolyl cis-trans isomerase G

UNKNOW

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