9B62 image
Deposition Date 2024-03-23
Release Date 2024-10-16
Last Version Date 2025-07-30
Entry Detail
PDB ID:
9B62
Title:
Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Exportin-1
Gene (Uniprot):XPO1
Chain IDs:A
Chain Length:1074
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTP-binding nuclear protein Ran
Gene (Uniprot):RAN
Mutagens:Q69L
Chain IDs:B, F
Chain Length:222
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SUMO-conjugating enzyme UBC9
Gene (Uniprot):UBE2I
Chain IDs:C
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ubiquitin-related modifier 1
Gene (Uniprot):SUMO1
Mutagens:Q94P
Chain IDs:D
Chain Length:101
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 SUMO-protein ligase RanBP2
Gene (Uniprot):RANBP2
Chain IDs:E
Chain Length:619
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ran GTPase-activating protein 1
Gene (Uniprot):RANGAP1
Chain IDs:G
Chain Length:591
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase.
Nat Commun 16 6403 6403 (2025)
PMID: 40640138 DOI: 10.1038/s41467-025-61694-1

Abstact

The human nucleoporin RanBP2/Nup358 interacts with SUMO1-modified RanGAP1 and the SUMO E2 Ubc9 at the nuclear pore complex (NPC) to promote export and disassembly of exportin Crm1/Ran(GTP)/cargo complexes. In mitosis, RanBP2/SUMO1-RanGAP1/Ubc9 remains intact after NPC disassembly and is recruited to kinetochores and mitotic spindles by Crm1 where it contributes to mitotic progression. RanBP2 binds SUMO1-RanGAP1/Ubc9 via motifs that also catalyze SUMO E3 ligase activity. Here, we resolve cryo-EM structures of a RanBP2 C-terminal fragment in complex with Crm1, SUMO1-RanGAP1/Ubc9, and two molecules of Ran(GTP). These structures reveal several interactions with Crm1 including a nuclear export signal (NES) for RanGAP1, the deletion of which mislocalizes RanGAP1 and the Ran GTPase in cells. Our structural and biochemical results support models in which RanBP2 E3 ligase activity is dependent on Crm1, the RanGAP1 NES and Ran GTPase cycling.

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Primary Citation of related structures