SMTL ID : 6ah0.1

The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 5.70 Å

Oligo State

hetero-1-1-3-3-3-3-3-3-3-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-functional Binders)

IHP.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

GTP.2: 17 residues within 4Å: Ligands: MG.3 Chain t: P.335 Chain u: L.138, H.139, G.141, K.142, T.143, C.144, G.180, T.205, P.206, G.207, K.259, S.311, S.312, Q.313, Y.314 10 PLIP interactions: 10 interactions with chain u Hydrogen bonds: u:H.139, u:G.141, u:K.142, u:T.143, u:C.144, u:G.180, u:T.205, u:G.207, u:Q.313, u:Y.314

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Ligands: GTP.2 Chain u: T.143 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, X. et al., Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Cell Res. (2018)

Release Date

2018-11-14

Peptides

U5 small nuclear ribonucleoprotein 200 kDa helicase: B
U5 small nuclear ribonucleoprotein 40 kDa protein: C
Small nuclear ribonucleoprotein Sm D2: DZl
Small nuclear ribonucleoprotein F: E0m
Small nuclear ribonucleoprotein E: F1n
Small nuclear ribonucleoprotein G: G2o
Small nuclear ribonucleoprotein Sm D3: HWp
Small nuclear ribonucleoprotein-associated proteins B and B': IXq
Small nuclear ribonucleoprotein Sm D1: JYr
U6 snRNA-associated Sm-like protein LSm2: L
U6 snRNA-associated Sm-like protein LSm3: M
U6 snRNA-associated Sm-like protein LSm4: N
U6 snRNA-associated Sm-like protein LSm5: O
U6 snRNA-associated Sm-like protein LSm6: P
U6 snRNA-associated Sm-like protein LSm7: Q
U6 snRNA-associated Sm-like protein LSm8: R
U2 small nuclear ribonucleoprotein A': U
U2 small nuclear ribonucleoprotein B'': V
Splicing factor 3A subunit 1: 3
Splicing factor 3A subunit 2: 4
Splicing factor 3A subunit 3: 5
Splicing factor 3B subunit 1: 6
Splicing factor 3B subunit 2: 7
Splicing factor 3B subunit 3: 8
Splicing factor 3B subunit 4: 9
Splicing factor 3B subunit 6: a
PHD finger-like domain-containing protein 5A: b
Splicing factor 3B subunit 5: c
U4/U6 small nuclear ribonucleoprotein Prp3: d
U4/U6 small nuclear ribonucleoprotein Prp4: e
Pre-mRNA-processing factor 6: f
U4/U6 small nuclear ribonucleoprotein Prp31: g
NHP2-like protein 1: h
Thioredoxin-like protein 4A: i
U4/U6.U5 tri-snRNP-associated protein 2: j
Probable ATP-dependent RNA helicase DDX23: s
Pre-mRNA-processing-splicing factor 8: t
116 kDa U5 small nuclear ribonucleoprotein component: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
D

C
E

D
a

Z
k

l
P

E
b

0
m

m
Q

F
c

1
l

n
R

G
d

2
n

o
S

H
e

W
h

p
T

I
f

X
i

q
U

J
g

Y
j

r
V

L
q

M
r

N
s

O
t

P
x

Q
y

R
z

U
o

V
p

3
u

4
v

5
w

6
1

7
2

8
3

9
4

a
5

b
6

c
7

d
J

e
K

f
N

g
L

h
M

i
O

j
W

s
X

t
A

u
C

U5 small nuclear ribonucleoprotein 200 kDa helicase

U5 small nuclear ribonucleoprotein 40 kDa protein

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D1

U6 snRNA-associated Sm-like protein LSm2

U6 snRNA-associated Sm-like protein LSm3

U6 snRNA-associated Sm-like protein LSm4

U6 snRNA-associated Sm-like protein LSm5

U6 snRNA-associated Sm-like protein LSm6

U6 snRNA-associated Sm-like protein LSm7

U6 snRNA-associated Sm-like protein LSm8

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Splicing factor 3A subunit 1

Splicing factor 3A subunit 2

Splicing factor 3A subunit 3

Splicing factor 3B subunit 1

Splicing factor 3B subunit 2

Splicing factor 3B subunit 3

Splicing factor 3B subunit 4

Splicing factor 3B subunit 6

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 5

U4/U6 small nuclear ribonucleoprotein Prp3

U4/U6 small nuclear ribonucleoprotein Prp4

Pre-mRNA-processing factor 6

U4/U6 small nuclear ribonucleoprotein Prp31

NHP2-like protein 1

Thioredoxin-like protein 4A

U4/U6.U5 tri-snRNP-associated protein 2

Probable ATP-dependent RNA helicase DDX23

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

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