SMTL ID : 8q7x.1

Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 4)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain D: K.142, T.143, G.180 Ligands: GTP.2 No protein-ligand interaction detected (PLIP)

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

GTP.2: 23 residues within 4Å: Chain B: P.335 Chain D: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, V.179, G.180, P.206, G.207, H.208, N.258, K.259, D.261, R.262, E.266, S.311, S.312, Q.313 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:H.139, D:H.140, D:G.141, D:K.142, D:T.143, D:C.144, D:D.164, D:D.164, D:G.180, D:G.207, D:N.258, D:K.259, D:K.259, D:S.311, D:S.312, D:Q.313 Salt bridges: D:H.139, D:K.142, D:K.142, D:D.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riabov Bassat, D. et al., Structural basis of human U5 snRNP late biogenesis and recycling. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-04-17

Peptides

Pre-mRNA-processing-splicing factor 8: B
U5 small nuclear ribonucleoprotein 200 kDa helicase: C
116 kDa U5 small nuclear ribonucleoprotein component: D
U5 small nuclear ribonucleoprotein 40 kDa protein: E
Probable ATP-dependent RNA helicase DDX23: F
Pre-mRNA-processing factor 6: G
CD2 antigen cytoplasmic tail-binding protein 2: H
Small nuclear ribonucleoprotein Sm D1: I
Small nuclear ribonucleoprotein-associated proteins B and B': J
Small nuclear ribonucleoprotein Sm D2: K
Small nuclear ribonucleoprotein Sm D3: L
Small nuclear ribonucleoprotein E: M
Small nuclear ribonucleoprotein F: N
Small nuclear ribonucleoprotein G: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
a

J
b

K
c

L
d

M
e

N
f

O
g

Pre-mRNA-processing-splicing factor 8

U5 small nuclear ribonucleoprotein 200 kDa helicase

116 kDa U5 small nuclear ribonucleoprotein component

U5 small nuclear ribonucleoprotein 40 kDa protein

Probable ATP-dependent RNA helicase DDX23

Pre-mRNA-processing factor 6

CD2 antigen cytoplasmic tail-binding protein 2

Small nuclear ribonucleoprotein Sm D1

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein G

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