SMTL ID : 6qdv.1

Human post-catalytic P complex spliceosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 6 residues within 4Å: Chain C: G.54, G.72, U.74 Chain K: G.12, C.13 Ligands: MG.5 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain C: A.53, G.54, U.74 Chain K: C.13, U.14 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain C: G.75, A.76 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: G.72, G.75 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain C: G.54, C.55, G.71 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: T.68, D.166, E.167 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.68 MG.10: 5 residues within 4Å: Chain I: T.88, D.114, D.149, T.150 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.88

1 x K: POTASSIUM ION(Non-functional Binders)

K.6: 5 residues within 4Å: Chain C: A.47, A.48, A.50, U.51, U.52 No protein-ligand interaction detected (PLIP)

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

ATP.8: 21 residues within 4Å: Chain D: F.19, Y.35, F.37, K.39, Q.44, Q.62, S.63, G.64, T.65, G.66, K.67, T.68, A.69, E.167, G.319, D.321, P.323, R.346, R.349, Y.350 Ligands: MG.7 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:Q.44, D:Q.44, D:G.64, D:T.65, D:G.66, D:K.67, D:T.68, D:A.69, D:G.319, D:D.321 Salt bridges: D:K.67, D:K.67, D:R.346, D:R.349, D:R.349, D:R.349 pi-Stacking: D:F.37, D:F.37, D:Y.350, D:Y.350

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

GTP.9: 25 residues within 4Å: Chain G: P.335 Chain I: L.83, H.84, H.85, G.86, K.87, T.88, C.89, D.109, C.111, G.123, V.124, G.125, P.151, G.152, H.153, N.203, K.204, D.206, R.207, E.211, S.256, S.257, Q.258 Ligands: MG.10 26 PLIP interactions: 26 interactions with chain I Hydrogen bonds: I:H.84, I:H.85, I:G.86, I:K.87, I:T.88, I:T.88, I:C.89, I:D.109, I:D.109, I:G.123, I:G.125, I:G.152, I:H.153, I:K.204, I:K.204, I:E.211, I:S.257, I:Q.258, I:Q.258 Salt bridges: I:H.84, I:H.84, I:H.84, I:K.87, I:K.87, I:D.206 pi-Cation interactions: I:K.204

7 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain R: C.105, C.117, C.119, C.134 Ligands: ZN.12, ZN.13 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.105, R:C.117, R:C.119, R:C.134 ZN.12: 6 residues within 4Å: Chain R: C.101, C.102, C.105, C.137 Ligands: ZN.11, ZN.13 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.101, R:C.102, R:C.105, R:C.137 ZN.13: 6 residues within 4Å: Chain R: C.101, C.119, C.139, C.142 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.101, R:C.119, R:C.139, R:C.142 ZN.14: 4 residues within 4Å: Chain S: C.7, C.10, C.64, C.67 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.7, S:C.10, S:C.64, S:C.67 ZN.15: 4 residues within 4Å: Chain S: C.28, C.31, C.54, C.57 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.28, S:C.31, S:C.54, S:C.57 ZN.16: 4 residues within 4Å: Chain S: C.148, C.156, C.162, H.166 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.148, S:C.156, S:C.162, S:H.166 ZN.18: 4 residues within 4Å: Chain 5: C.120, C.123, H.128, C.133 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.120, 5:C.123, 5:H.128, 5:C.133

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Covalent)

IHP.17: 15 residues within 4Å: Chain 5: Y.163, K.166, R.167 Chain G: R.163, K.442, Y.580, H.584, Q.587, K.609, H.610, Y.613, Y.614, N.617, K.623, G.624 20 PLIP interactions: 14 interactions with chain G, 6 interactions with chain 5 Hydrogen bonds: G:Q.587, G:Y.614, G:N.617, 5:R.167 Salt bridges: G:R.163, G:K.442, G:K.442, G:K.442, G:H.584, G:H.584, G:K.609, G:K.609, G:K.609, G:H.610, G:K.623, 5:K.166, 5:K.166, 5:K.166, 5:R.167, 5:R.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fica, S.M. et al., A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Science (2019)

Release Date

2019-02-20

Peptides

Eukaryotic initiation factor 4A-III, N-terminally processed: D
RNA-binding protein 8A: E
Protein mago nashi homolog 2: F
Pre-mRNA-processing-splicing factor 8: G
U5 small nuclear ribonucleoprotein 200 kDa helicase: H
116 kDa U5 small nuclear ribonucleoprotein component: I
PRKR-interacting protein 1: J
Cactin: L
Protein FAM32A: M
Pre-mRNA-splicing factor CWC22 homolog: N
Pleiotropic regulator 1: P
SNW domain-containing protein 1: Q
Protein BUD31 homolog: R
Pre-mRNA-splicing factor RBM22: S
U5 small nuclear ribonucleoprotein 40 kDa protein: T
Cell division cycle 5-like protein: U
Spliceosome-associated protein CWC15 homolog: V
Serine/arginine repetitive matrix protein 2: W
Crooked neck-like protein 1: X
Pre-mRNA-splicing factor SYF1: Y
Intron-binding protein aquarius: Z
ATP-dependent RNA helicase DHX8: 0
U2 small nuclear ribonucleoprotein A': 1
U2 small nuclear ribonucleoprotein B'': 2
NF-kappa-B-activating protein: 3
Small nuclear ribonucleoprotein-associated proteins B and B': 4d
Pre-mRNA-splicing factor SLU7: 5
Small nuclear ribonucleoprotein Sm D3: 6g
Small nuclear ribonucleoprotein E: 7i
Small nuclear ribonucleoprotein F: 8j
Small nuclear ribonucleoprotein G: 9k
Small nuclear ribonucleoprotein Sm D1: ae
Peptidyl-prolyl cis-trans isomerase-like 1: b
Small nuclear ribonucleoprotein Sm D2: cf
Pre-mRNA-processing factor 17: h
Pre-mRNA-splicing factor SPF27: l
Pre-mRNA-processing factor 19: mnop
Pre-mRNA-splicing factor SYF2: q
Replication stress response regulator SDE2: r

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
7

E
8

F
9

G
A

H
B

I
C

J
D

L
F

M
G

N
H

P
J

Q
K

R
L

S
M

T
N

U
O

V
P

W
R

X
S

Y
T

Z
U

0
V

1
W

2
Y

3
Z

4
b

d
k

5
c

6
d

g
n

7
e

i
p

8
f

j
q

9
g

k
r

a
h

e
l

b
i

c
j

f
m

h
o

l
s

m
t

n
u

o
v

p
w

q
y

r
z

Eukaryotic initiation factor 4A-III, N-terminally processed

RNA-binding protein 8A

Protein mago nashi homolog 2

Pre-mRNA-processing-splicing factor 8

U5 small nuclear ribonucleoprotein 200 kDa helicase

116 kDa U5 small nuclear ribonucleoprotein component

PRKR-interacting protein 1

Cactin

Protein FAM32A

Pre-mRNA-splicing factor CWC22 homolog

Pleiotropic regulator 1

SNW domain-containing protein 1

Protein BUD31 homolog

Pre-mRNA-splicing factor RBM22

U5 small nuclear ribonucleoprotein 40 kDa protein

Cell division cycle 5-like protein

Spliceosome-associated protein CWC15 homolog

Serine/arginine repetitive matrix protein 2

Crooked neck-like protein 1

Pre-mRNA-splicing factor SYF1

Intron-binding protein aquarius

ATP-dependent RNA helicase DHX8

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

NF-kappa-B-activating protein

Small nuclear ribonucleoprotein-associated proteins B and B'

Pre-mRNA-splicing factor SLU7

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D1

Peptidyl-prolyl cis-trans isomerase-like 1

Small nuclear ribonucleoprotein Sm D2

Pre-mRNA-processing factor 17

Pre-mRNA-splicing factor SPF27

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SYF2

Replication stress response regulator SDE2

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