SMTL ID : 6icz.1

Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 14 residues within 4Å: Chain E: R.163, K.442, Y.580, H.584, K.606, K.609, H.610, Y.613, Y.614, N.617, K.623, G.624 Chain Y: K.166, R.167 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain Y Hydrogen bonds: E:Y.613, E:N.617 Salt bridges: E:R.163, E:K.442, E:K.442, E:K.442, E:H.584, E:H.584, E:K.609, E:K.609, E:K.609, E:H.610, E:K.623, Y:K.166, Y:K.166, Y:R.167, Y:R.167

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

GTP.2: 22 residues within 4Å: Chain E: P.335 Chain G: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, V.179, G.180, P.206, G.207, H.208, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:H.139, G:H.140, G:G.141, G:K.142, G:T.143, G:T.143, G:C.144, G:D.164, G:D.164, G:G.180, G:G.207, G:H.208, G:K.259, G:S.312, G:Q.313 Salt bridges: G:H.139, G:H.139, G:H.139, G:K.142, G:K.142, G:D.261

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

MG.3: 2 residues within 4Å: Chain G: T.143 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.143 MG.4: 4 residues within 4Å: Chain I: G.54, G.72, U.74 Chain J: G.59 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain I: A.53, G.54, U.74 Chain J: G.227 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain I: U.57, G.75 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain I: A.56, G.75 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain I: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain I: A.48, A.50 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain 1: D.160 No protein-ligand interaction detected (PLIP)

7 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain O: C.105, C.117, C.119, C.134 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.105, O:C.117, O:C.119, O:C.134 ZN.11: 6 residues within 4Å: Chain O: C.101, C.102, C.105, C.137 Ligands: ZN.10, ZN.12 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.102, O:C.105, O:C.137 ZN.12: 5 residues within 4Å: Chain O: C.101, C.119, C.139, C.142 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.101, O:C.119, O:C.139, 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.16: 5 residues within 4Å: Chain Y: C.120, N.122, C.123, H.128, C.133 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.120, Y:C.123, Y:H.128, Y:C.133

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

ATP.17: 11 residues within 4Å: Chain 1: Q.801, F.802, T.803, P.825, G.826, T.827, G.828, K.829, T.830, G.1137 Ligands: MG.18 7 PLIP interactions: 7 interactions with chain 1 Hydrogen bonds: 1:Q.801, 1:T.803, 1:G.826, 1:T.827, 1:G.828, 1:K.829, 1:T.830

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structures of the human spliceosomes before and after release of the ligated exon. Cell Res. (2019)

Release Date

2019-03-13

Peptides

Protein mago nashi homolog 2: A
RNA-binding protein 8A: B
Eukaryotic initiation factor 4A-III: C
Protein CASC3: D
Pre-mRNA-processing-splicing factor 8: E
116 kDa U5 small nuclear ribonucleoprotein component: G
U5 small nuclear ribonucleoprotein 40 kDa protein: H
Crooked neck-like protein 1: 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
Serine/arginine repetitive matrix protein 2: U
Pre-mRNA-splicing factor CWC22 homolog: V
Pre-mRNA-processing factor 17: W
PRKR-interacting protein 1: X
Pre-mRNA-splicing factor SLU7: Y
Pre-mRNA-splicing factor SYF1: Z
Peptidyl-prolyl cis-trans isomerase E: 0
RNA helicase aquarius: 1
Small nuclear ribonucleoprotein Sm D3: 2c
Small nuclear ribonucleoprotein-associated protein: 3d
Small nuclear ribonucleoprotein Sm D1: 4e
Small nuclear ribonucleoprotein Sm D2: 5f
Small nuclear ribonucleoprotein F: 6g
Small nuclear ribonucleoprotein E: 7h
Small nuclear ribonucleoprotein G: 8i
U2 small nuclear ribonucleoprotein A': 9
U2 small nuclear ribonucleoprotein B'': a
ATP-dependent RNA helicase DHX8: b
Pre-mRNA-splicing factor SPF27: j
Pre-mRNA-processing factor 19: klmn
U5 small nuclear ribonucleoprotein 200 kDa helicase: o

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
v

B
w

C
u

D
x

E
A

G
C

H
E

L
J

M
L

N
M

O
N

P
O

Q
P

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Z

Z
I

0
y

1
Q

2
h

c
a

3
i

d
b

4
j

e
c

5
k

f
d

6
m

g
f

7
l

h
e

8
n

i
g

9
o

a
p

b
Y

j
K

k
q

l
r

m
s

n
t

o
D

Protein mago nashi homolog 2

RNA-binding protein 8A

Eukaryotic initiation factor 4A-III

Protein CASC3

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

PRKR-interacting protein 1

Pre-mRNA-splicing factor SLU7

Pre-mRNA-splicing factor SYF1

Peptidyl-prolyl cis-trans isomerase E

RNA helicase aquarius

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated protein

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''

ATP-dependent RNA helicase DHX8

Pre-mRNA-splicing factor SPF27

Pre-mRNA-processing factor 19

U5 small nuclear ribonucleoprotein 200 kDa helicase

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