SMTL ID : 7abg.1

Human pre-Bact-1 spliceosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 3 residues within 4Å: Chain Y: K.623, G.624, P.625 No protein-ligand interaction detected (PLIP)

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.2: 19 residues within 4Å: Ligands: MG.3 Chain c: L.138, H.139, H.140, G.141, K.142, T.143, C.144, G.178, V.179, G.180, P.206, G.207, K.259, I.260, R.262, S.311, S.312, Q.313 11 PLIP interactions: 11 interactions with chain c Hydrogen bonds: c:L.138, c:H.139, c:G.141, c:K.142, c:T.143, c:C.144, c:G.180, c:I.260, c:R.262, c:S.312, c:Q.313

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x GTG: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE(Covalent)

GTG.4: 18 residues within 4Å: Chain J: Y.20, Q.23, Y.43, D.114, W.115, D.116, R.123, Y.125, G.126, R.127, G.128, Q.133, V.134, R.135, Y.138 Chain f: C.148, Y.149, A.150 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain f Hydrogen bonds: J:W.115, J:R.123, J:R.127, J:G.128, J:V.134, f:A.150, f:A.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Townsend, C. et al., Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Science (2020)

Release Date

2020-12-23

Peptides

Nuclear cap-binding protein subunit 1: A
U6 snRNA-associated Sm-like protein LSm7: B
Splicing factor 3B subunit 6: C
Splicing factor 3A subunit 2: D
U5 small nuclear ribonucleoprotein 40 kDa protein: E
U2 small nuclear ribonucleoprotein A': F
U2 small nuclear ribonucleoprotein B'': G
U5 small nuclear ribonucleoprotein 200 kDa helicase: H
Protein BUD31 homolog: I
Nuclear cap-binding protein subunit 2: J
Cell division cycle 5-like protein: L
Spliceosome-associated protein CWC15 homolog: M
U6 snRNA-associated Sm-like protein LSm2: N
U6 snRNA-associated Sm-like protein LSm3: O
U6 snRNA-associated Sm-like protein LSm4: P
U6 snRNA-associated Sm-like protein LSm5: Q
U6 snRNA-associated Sm-like protein LSm6: R
U6 snRNA-associated Sm-like protein LSm8: T
Microfibrillar-associated protein 1: U
PHD finger-like domain-containing protein 5A: V
Pleiotropic regulator 1: W
Pre-mRNA-processing-splicing factor 8: Y
Pre-mRNA-splicing factor 38A: Z
Pre-mRNA-splicing factor RBM22: 0
Splicing factor 3A subunit 1: 1
Splicing factor 3A subunit 3: 2
Transcription elongation regulator 1: 3
Splicing factor 3B subunit 1: 4
Splicing factor 3B subunit 2: 5
Splicing factor 3B subunit 3: 6
Splicing factor 3B subunit 4: 7
Splicing factor 3B subunit 5: 8
SNW domain-containing protein 1: 9
Smad nuclear-interacting protein 1: a
Zinc finger matrin-type protein 2: b
116 kDa U5 small nuclear ribonucleoprotein component: c
Serine/arginine repetitive matrix protein 1: d
Serine/arginine-rich splicing factor 1: f
Small nuclear ribonucleoprotein Sm D2: gp
Small nuclear ribonucleoprotein F: hs
Small nuclear ribonucleoprotein-associated proteins B and B': in
Small nuclear ribonucleoprotein Sm D3: jq
Small nuclear ribonucleoprotein G: kt
Small nuclear ribonucleoprotein E: lr
Small nuclear ribonucleoprotein Sm D1: mo
Ubiquitin-like protein 5: u
WW domain-binding protein 11: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A5

B
A2

C
z

D
F

E
D

F
W

G
B

H
s

I
Q

J
A1

L
L

M
R

N
V

O
9

P
C

Q
H

R
J

T
A3

U
K

V
y

W
G

Y
A

Z
I

0
P

1
p

2
4

3
A4

4
u

5
T

6
E

7
w

8
x

9
v

a
0

b
N

c
r

d
Y

f
A6

g
h

p
a

h
i

s
b

i
m

n
f

j
l

q
e

k
k

t
d

l
j

r
c

m
n

o
g

u
q

v
X

Nuclear cap-binding protein subunit 1

U6 snRNA-associated Sm-like protein LSm7

Splicing factor 3B subunit 6

Splicing factor 3A subunit 2

U5 small nuclear ribonucleoprotein 40 kDa protein

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

U5 small nuclear ribonucleoprotein 200 kDa helicase

Protein BUD31 homolog

Nuclear cap-binding protein subunit 2

Cell division cycle 5-like protein

Spliceosome-associated protein CWC15 homolog

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 LSm8

Microfibrillar-associated protein 1

PHD finger-like domain-containing protein 5A

Pleiotropic regulator 1

Pre-mRNA-processing-splicing factor 8

Pre-mRNA-splicing factor 38A

Pre-mRNA-splicing factor RBM22

Splicing factor 3A subunit 1

Splicing factor 3A subunit 3

Transcription elongation regulator 1

Splicing factor 3B subunit 1

Splicing factor 3B subunit 2

Splicing factor 3B subunit 3

Splicing factor 3B subunit 4

Splicing factor 3B subunit 5

SNW domain-containing protein 1

Smad nuclear-interacting protein 1

Zinc finger matrin-type protein 2

116 kDa U5 small nuclear ribonucleoprotein component

Serine/arginine repetitive matrix protein 1

Serine/arginine-rich splicing factor 1

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein Sm D1

Ubiquitin-like protein 5

WW domain-binding protein 11

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