SMTL ID : 5xjc.1

Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain A: R.163, K.442, H.584, K.609, H.610, Y.613, K.623, G.624 Chain Z: K.166, R.167 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain Z Salt bridges: 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, Z:K.166, Z:K.166, Z:R.167, Z:R.167 Hydrogen bonds: Z:R.167

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 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:H.139, C:G.141, C:K.142, C:T.143, C:C.144, C:G.180, C:G.207, C:H.208, C:Q.313 Salt bridges: C:D.261

11 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: 4 residues within 4Å: Chain D: T.1357, D.1454, E.1455 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.1454 MG.7: 4 residues within 4Å: Chain F: G.54, G.72, U.74 Chain G: G.61 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain F: U.52, A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain F: G.75 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain F: G.71, G.75 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain F: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: A.48, A.50 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain Q: T.830, Q.861 Ligands: ATP.19 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain Q: D.160 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Ligands: ATP.24 Chain k: T.89, D.187, E.188 1 PLIP interactions: 1 interactions with chain k Metal complexes: k:T.89

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

ADP.4: 11 residues within 4Å: Chain D: T.480, N.482, Q.485, G.506, A.507, G.508, K.509, T.510, D.615, E.616, N.820 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.482, D:Q.485, D:Q.485, D:G.506, D:G.508, D:K.509, D:T.510, D:D.615, D:E.616, D:N.820 Salt bridges: D:K.509, D:K.509 ADP.5: 14 residues within 4Å: Chain D: F.1325, F.1327, F.1328, Q.1332, T.1352, G.1353, S.1354, G.1355, K.1356, T.1357, I.1358, E.1455, P.1694 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:F.1327, D:N.1329, D:Q.1332, D:G.1353, D:S.1354, D:G.1355, D:K.1356, D:T.1357 Salt bridges: D:K.1356, D:K.1356 pi-Stacking: D:F.1325

7 x ZN: ZINC ION(Non-covalent)

ZN.13: 5 residues within 4Å: Chain N: C.105, C.117, C.119, C.134 Ligands: ZN.14 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.105, N:C.117, N:C.119, N:C.134 ZN.14: 6 residues within 4Å: Chain N: C.101, C.102, C.105, C.137 Ligands: ZN.13, ZN.15 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.101, N:C.102, N:C.105, N:C.137 ZN.15: 5 residues within 4Å: Chain N: C.101, C.119, C.139, C.142 Ligands: ZN.14 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.101, N:C.119, N:C.139, N:C.142 ZN.16: 5 residues within 4Å: Chain O: C.24, C.27, C.81, T.83, C.84 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.24, O:C.27, O:C.81, O:C.84 ZN.17: 4 residues within 4Å: Chain O: C.45, C.48, C.71, C.74 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.45, O:C.48, O:C.71, O:C.74 ZN.18: 4 residues within 4Å: Chain O: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.165, O:C.173, O:C.179, O:H.183 ZN.22: 5 residues within 4Å: Chain Z: C.120, N.122, C.123, H.128, C.133 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.120, Z:C.123, Z:H.128, Z:C.133

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

ATP.19: 17 residues within 4Å: Chain Q: I.800, Q.801, F.802, T.803, Q.806, P.825, G.826, T.827, G.828, K.829, T.830, D.831, G.1137, R.1138, L.1157, H.1159 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain Q Hydrogen bonds: Q:T.803, Q:Q.806, Q:Q.806, Q:G.826, Q:T.827, Q:G.828, Q:K.829, Q:T.830, Q:T.830, Q:T.830, Q:K.865, Q:K.865, Q:H.1159 Salt bridges: Q:K.829, Q:K.829 ATP.24: 21 residues within 4Å: Ligands: MG.23 Chain k: 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 21 PLIP interactions: 21 interactions with chain k Hydrogen bonds: k:Q.65, k:Q.65, k:G.85, k:T.86, k:G.87, k:K.88, k:T.89, k:T.89, k:A.90, k:G.340, k:D.342 Salt bridges: k:K.88, k:K.88, k:R.367, k:R.370, k:R.370, k:R.370 pi-Stacking: k:F.58, k:F.58, k:Y.371, k:Y.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., An Atomic Structure of the Human Spliceosome. Cell (2017)

Release Date

2017-07-05

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 SYF2: M
Protein BUD31 homolog: N
Pre-mRNA-splicing factor RBM22: O
Spliceosome-associated protein CWC15 homolog: P
Intron-binding protein aquarius: 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
ATP-dependent RNA helicase DHX8: Y
Pre-mRNA-splicing factor SLU7: Z
Small nuclear ribonucleoprotein Sm D3: 07
Small nuclear ribonucleoprotein-associated proteins B and B': 18
Small nuclear ribonucleoprotein Sm D1: 29
Small nuclear ribonucleoprotein Sm D2: 3a
Small nuclear ribonucleoprotein F: 4b
Small nuclear ribonucleoprotein E: 5c
Small nuclear ribonucleoprotein G: 6d
U2 small nuclear ribonucleoprotein A': e
U2 small nuclear ribonucleoprotein B'': f
Pre-mRNA-processing factor 19: ghij
Eukaryotic initiation factor 4A-III: k
Protein mago nashi homolog 2: l
RNA-binding protein 8A: m
Protein CASC3: n

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
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

7
h

1
b

8
i

2
c

9
j

3
d

a
k

4
f

b
m

5
e

c
l

6
g

d
n

e
o

f
p

g
q

h
r

i
s

j
t

k
u

l
v

m
w

n
x

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

Intron-binding protein 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

PRKR-interacting protein 1

ATP-dependent RNA helicase DHX8

Pre-mRNA-splicing factor SLU7

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''

Pre-mRNA-processing factor 19

Eukaryotic initiation factor 4A-III

Protein mago nashi homolog 2

RNA-binding protein 8A

Protein CASC3

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