5DHF

Crystal Structure of hRio2 NES Peptide in complex with CRM1-Ran-RanBP1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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This is version 1.5 of the entry. See complete history. 


Literature

Structural determinants of nuclear export signal orientation in binding to exportin CRM1.

Fung, H.Y., Fu, S.C., Brautigam, C.A., Chook, Y.M.

(2015) Elife 4

  • DOI: https://doi.org/10.7554/eLife.10034
  • Primary Citation of Related Structures:  
    5DH9, 5DHA, 5DHF, 5DI9, 5DIF

  • PubMed Abstract: 

    • The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove ...

    The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). Comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.

    Organizational Affiliation: 

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanA237Homo sapiensMutation(s): 0 
Gene Names: RAN, ARA24, OK/SW-cl.81
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
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PHAROS:  P62826
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UniProt GroupP62826
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1B143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-1C1,024Saccharomyces cerevisiae S288CMutation(s): 6 
Gene Names: CRM1, KAP124, XPO1, YGR218W, G8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase RIO2D19Homo sapiensMutation(s): 0 
Gene Names: RIOK2, RIO2
EC: 2.7.11.1
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Find proteins for Q9BVS4 (Homo sapiens)
Explore Q9BVS4 
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PHAROS:  Q9BVS4
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.479α = 90
b = 106.479β = 90
c = 303.731γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
HKL-3000data collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Croucher FoundationHong KongStudent Scholarship
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069909
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP120352
University of Texas SouthwesternUnited StatesEndowed Scholars Program
Welch FoundationUnited StatesI-1532
Leukemia & Lymphoma SocietyUnited StatesScholar Award

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Other
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-04-24
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence