9B62 | pdb_00009b62

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

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2024-03-23 Released: 2024-10-16 
  • Deposition Author(s): Lima, C.D., DiMattia, M.A.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase.

Baytshtok, V.DiMattia, M.A.Lima, C.D.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.10.04.616749
  • Primary Citation of Related Structures:  
    9B62

  • PubMed Abstract: 

    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. Interestingly, 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 unanticipated 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.


  • Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-11,074Homo sapiensMutation(s): 0 
Gene Names: XPO1CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens)
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Go to UniProtKB:  O14980
PHAROS:  O14980
GTEx:  ENSG00000082898 
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UniProt GroupO14980
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran
B, F
222Homo sapiensMutation(s): 1 
Gene Names: RANARA24OK/SW-cl.81
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
GTEx:  ENSG00000132341 
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UniProt GroupP62826
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9161Homo sapiensMutation(s): 0 
Gene Names: UBE2IUBC9UBCE9
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens)
Explore P63279 
Go to UniProtKB:  P63279
PHAROS:  P63279
GTEx:  ENSG00000103275 
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UniProt GroupP63279
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1101Homo sapiensMutation(s): 1 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
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UniProt GroupP63165
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
E3 SUMO-protein ligase RanBP2619Homo sapiensMutation(s): 0 
Gene Names: RANBP2NUP358
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P49792 (Homo sapiens)
Explore P49792 
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PHAROS:  P49792
GTEx:  ENSG00000153201 
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UniProt GroupP49792
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1591Homo sapiensMutation(s): 0 
Gene Names: RANGAP1KIAA1835SD
UniProt & NIH Common Fund Data Resources
Find proteins for P46060 (Homo sapiens)
Explore P46060 
Go to UniProtKB:  P46060
PHAROS:  P46060
GTEx:  ENSG00000100401 
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UniProt GroupP46060
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118080

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references