SMTL ID : 9b62.1

Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 26 residues within 4Å: Chain B: G.25, G.26, T.27, G.28, K.29, T.30, T.31, F.41, E.42, K.43, K.44, Y.45, V.46, A.47, T.48, T.72, A.73, G.74, N.128, K.129, D.131, I.132, S.156, A.157, K.158 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.26, B:T.27, B:T.27, B:G.28, B:K.29, B:T.30, B:T.30, B:T.31, B:E.42, B:Y.45, B:T.48, B:G.74, B:N.128, B:K.129, B:K.129, B:A.157, B:K.158 Salt bridges: B:K.29, B:K.29, B:D.131 pi-Stacking: B:F.41, B:F.41 GTP.3: 24 residues within 4Å: Chain F: G.25, G.26, T.27, G.28, K.29, T.30, T.31, E.42, K.43, K.44, Y.45, A.47, T.48, T.72, G.74, L.75, N.128, K.129, D.131, I.132, S.156, A.157, K.158 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.26, F:T.27, F:G.28, F:K.29, F:T.30, F:T.31, F:K.43, F:K.44, F:T.48, F:G.74, F:N.128, F:K.129, F:A.157, F:K.158 Salt bridges: F:K.29, F:K.29, F:D.131 pi-Stacking: F:F.41, F:F.41

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: T.30, T.48, D.71 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.30, B:T.48 MG.4: 3 residues within 4Å: Chain F: T.30, T.48 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.30, F:T.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baytshtok, V. et al., Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase. Biorxiv (2024)

Release Date

2024-10-16

Peptides

Exportin-1: A
GTP-binding nuclear protein Ran: BF
SUMO-conjugating enzyme UBC9: C
Small ubiquitin-related modifier 1: D
E3 SUMO-protein ligase RanBP2: E
Ran GTPase-activating protein 1: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F
F

C
C

D
D

E
E

G
G

Exportin-1

GTP-binding nuclear protein Ran

SUMO-conjugating enzyme UBC9

Small ubiquitin-related modifier 1

E3 SUMO-protein ligase RanBP2

Ran GTPase-activating protein 1

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