6A38

MVM NS2 NES in complex with CRM1-Ran-RanBP1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Cancer Therapy with Nanoparticle-Medicated Intracellular Expression of Peptide CRM1-Inhibitor.

Sui, M., Xiong, M., Li, Y., Zhou, Q., Shen, X., Jia, D., Gou, M., Sun, Q.

(2021) Int J Nanomedicine 16: 2833-2847

  • DOI: https://doi.org/10.2147/IJN.S266398
  • Primary Citation of Related Structures:  
    6A38, 6A3A, 6A3B, 6A3C, 6A3E, 6KFT

  • PubMed Abstract: 

    Peptides can be rationally designed as non-covalent inhibitors for molecularly targeted therapy. However, it remains challenging to efficiently deliver the peptides into the targeted cells, which often severely affects their therapeutic efficiency.

    • Organizational Affiliation: 

    Department of Pathology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu, 610041, People's Republic of China.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran235Homo sapiensMutation(s): 1 
Gene Names: RAN, ARA24, OK/SW-cl.81
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
GTEx:  ENSG00000132341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62826
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41920 
Go to UniProtKB:  P41920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41920
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-11,003Saccharomyces cerevisiae S288CMutation(s): 5 
Gene Names: CRM1, KAP124, XPO1, YGR218W, G8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30822 
Go to UniProtKB:  P30822
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30822
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MVM NS2 NES20Minute virus of miceMutation(s): 0 
Gene Names: NS2
UniProt
Find proteins for P0DJZ2 (Murine minute virus (strain MVM prototype))
Explore P0DJZ2 
Go to UniProtKB:  P0DJZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJZ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth C],
I [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
J [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.438α = 90
b = 105.438β = 90
c = 303.066γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

  • Released Date: 2019-06-19 
    • Deposition Author(s): Sun, Q., Li, Y.
Funding OrganizationLocationGrant Number
National Science Foundation (China)China81502629

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description