SMTL ID : 7vpx.1

The cryo-EM structure of the human pre-A complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

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

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.56, C.59, T.61, H.72, H.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.56, A:C.59, A:H.72, A:H.78 ZN.2: 4 residues within 4Å: Chain K: C.408, C.411, H.425, H.431 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.408, K:H.425, K:H.431 ZN.3: 4 residues within 4Å: Chain 6: C.6, C.9, H.24, H.30 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.6, 6:C.9, 6:H.24, 6:H.30 ZN.4: 4 residues within 4Å: Chain 8: C.11, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.11, 8:C.46, 8:C.49, 8:C.85 ZN.5: 4 residues within 4Å: Chain 8: C.30, C.33, C.72, C.75 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.30, 8:C.33, 8:C.72, 8:C.75 ZN.6: 3 residues within 4Å: Chain 8: C.23, C.58, C.61 3 PLIP interactions: 3 interactions with chain 8 Metal complexes: 8:C.23, 8:C.58, 8:C.61

1 x SJT: spliceostatin A (form II)(Non-covalent)

SJT.7: 10 residues within 4Å: Chain 8: K.25, C.26, K.29, Y.36 Chain E: L.1066, R.1074, V.1078, Q.1107, V.1114, Y.1157 8 PLIP interactions: 4 interactions with chain 8, 4 interactions with chain E Hydrophobic interactions: 8:K.29, 8:Y.36, 8:Y.36, 8:Y.36, E:L.1066, E:V.1078, E:V.1114 Hydrogen bonds: E:L.1066

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structural insights into branch site proofreading by human spliceosome. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-05-03

Peptides

Splicing factor 3A subunit 2: A
Splicing factor 1: B
DnaJ homolog subfamily C member 8: C
Splicing factor 3B subunit 1: E
Splicing factor 3B subunit 2: F
Splicing factor 3B subunit 3: G
Splicing factor 3B subunit 4: H
Splicing factor 3B subunit 5: I
Splicing factor 3A subunit 1: J
Splicing factor 3A subunit 3: K
Probable ATP-dependent RNA helicase DDX46: L
U2 small nuclear ribonucleoprotein A': M
U2 small nuclear ribonucleoprotein B'': N
Small nuclear ribonucleoprotein Sm D2: O5
Small nuclear ribonucleoprotein F: PZ
Small nuclear ribonucleoprotein E: Q4
Small nuclear ribonucleoprotein G: R3
Small nuclear ribonucleoprotein Sm D3: S7
Small nuclear ribonucleoprotein-associated proteins B and B': T1
Small nuclear ribonucleoprotein Sm D1: U0
U1 small nuclear ribonucleoprotein 70 kDa: Y
U1 small nuclear ribonucleoprotein A: 2
U1 small nuclear ribonucleoprotein C: 6
PHD finger-like domain-containing protein 5A: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
J

E
1

F
2

G
3

H
4

I
5

J
A

K
C

L
E

M
F

N
G

O
a

5
i

P
b

Z
m

Q
c

4
l

R
d

3
n

S
e

7
j

T
f

1
k

U
g

0
h

Y
O

2
M

6
N

8
6

Splicing factor 3A subunit 2

Splicing factor 1

DnaJ homolog subfamily C member 8

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

Splicing factor 3A subunit 1

Splicing factor 3A subunit 3

Probable ATP-dependent RNA helicase DDX46

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

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

U1 small nuclear ribonucleoprotein 70 kDa

U1 small nuclear ribonucleoprotein A

U1 small nuclear ribonucleoprotein C

PHD finger-like domain-containing protein 5A

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