SMTL ID : 9hfl.1

Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 28 residues within 4Å: Chain A: M.886 Chain B: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, F.35, E.36, K.37, K.38, Y.39, V.40, A.41, T.42, A.67, G.68, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.20, B:T.21, B:T.21, B:G.22, B:K.23, B:T.24, B:T.24, B:T.25, B:T.25, B:Y.39, B:V.40, B:T.42, B:G.68, B:N.122, B:K.123, B:K.123, B:A.151, B:K.152 Salt bridges: B:K.23, B:K.23, B:D.125 pi-Stacking: B:F.35, B:F.35

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: K.23, T.24, T.42, D.65 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.24, B:T.42

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.3: 23 residues within 4Å: Chain D: Y.20, Y.43, F.83, F.85, R.112, D.114, W.115, D.116, R.123, Y.125, G.126, R.127, G.128, Q.133, V.134, Y.138 Chain F: D.144, S.146, R.147, Y.152, Y.154, K.158 Chain G: A.1 29 PLIP interactions: 19 interactions with chain D, 10 interactions with chain F Hydrogen bonds: D:Y.20, D:Y.20, D:Y.20, D:R.112, D:R.112, D:W.115, D:R.123, D:R.123, D:R.127, D:G.132, D:Q.133, D:V.134, F:S.146, F:R.147, F:Y.152 Water bridges: D:A.117, F:R.147, F:R.147, F:R.147 Salt bridges: D:D.114, D:D.116, D:R.127, F:R.147 pi-Stacking: D:Y.20, D:Y.43, D:Y.43, F:Y.154, F:Y.154 pi-Cation interactions: F:R.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubiez, E. et al., Structural basis for the synergistic assembly of the snRNA export complex. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-07-16

Peptides

Exportin-1: A
GTP-binding nuclear protein Ran: B
Nuclear cap-binding protein subunit 1: C
Nuclear cap-binding protein subunit 2: D
Phosphorylated adapter RNA export protein: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
N

F
P

Exportin-1

GTP-binding nuclear protein Ran

Nuclear cap-binding protein subunit 1

Nuclear cap-binding protein subunit 2

Phosphorylated adapter RNA export protein

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