1RRP

STRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

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


Literature

Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport.

Vetter, I.R., Nowak, C., Nishimoto, T., Kuhlmann, J., Wittinghofer, A.

(1999) Nature 398: 39-46

  • DOI: 10.1038/17969
  • Primary Citation of Related Structures:  
    1RRP

  • PubMed Abstract: 

    • The protein Ran is a small GTP-binding protein that binds to two types of effector inside the cell: Ran-binding proteins, which have a role in terminating export processes from the nucleus to the cytoplasm, and importin-beta-like molecules that bind cargo proteins during nuclear transport ...

    The protein Ran is a small GTP-binding protein that binds to two types of effector inside the cell: Ran-binding proteins, which have a role in terminating export processes from the nucleus to the cytoplasm, and importin-beta-like molecules that bind cargo proteins during nuclear transport. The Ran-binding domain is a conserved sequence motif found in several proteins that participate in these transport processes. The Ran-binding protein RanBP2 contains four of these domains and constitutes a large part of the cytoplasmic fibrils that extend from the nuclear-pore complex. The structure of Ran bound to a non-hydrolysable GTP analogue (Ran x GppNHp) in complex with the first Ran-binding domain (RanBD1) of human RanBP2 reveals not only that RanBD1 has a pleckstrin-homology domain fold, but also that the switch-I region of Ran x GppNHp resembles the canonical Ras GppNHp structure and that the carboxy terminus of Ran is wrapped around RanBD1, contacting a basic patch on RanBD1 through its acidic end. This molecular 'embrace' enables RanBDs to sequester the Ran carboxy terminus, triggering the dissociation of Ran x GTP from importin-beta-related transport factors and facilitating GTP hydrolysis by the GTPase-activating protein ranGAP. Such a mechanism represents a new type of switch mechanism and regulatory protein-protein interaction for a Ras-related protein.

    Related Citations: 
    • Ranbp1 is Crucial for the Release of Rangtp from Importin Beta-Related Nuclear Transport Factors
      Bischoff, F.R., Gorlich, D.
      (1997) FEBS Lett 419: 249
    • Dynamic and Equilibrium Studies on the Interaction of Ran with its Effector, Ranbp1
      Kuhlmann, J., Macara, I., Wittinghofer, A.
      (1997) Biochemistry 36: 12027
    • A Ran-Binding Motif Found in Nuclear Pore Proteins
      Hartmann, E., Gorlich, D.
      (1995) Trends Cell Biol 5: 192
    • A Giant Nucleopore Protein that Binds Ran/Tc4
      Yokoyama, N., Hayashi, N., Seki, T., Pante, N., Ohba, T., Nishii, K., Kuma, K., Hayashida, T., Miyata, T., Aebi, U., Fukui, M., Nishimoto, T.
      (1995) Nature 376: 184
    • The C Terminus of the Nuclear Ran/Tc4 Gtpase Stabilizes the Gdp-Bound State and Mediates Interactions with Rcc1, Ran-Gap, and Htf9A/Ranbp1
      Richards, S.A., Lounsbury, K.M., Macara, I.G.
      (1995) J Biol Chem 270: 14405
    • Co-Activation of Rangtpase and Inhibition of GTP Dissociation by Ran-GTP Binding Protein Ranbp1
      Bischoff, F.R., Krebber, H., Smirnova, E., Dong, W., Ponstingl, H.
      (1995) EMBO J 14: 705
    Organizational Affiliation: 

    Abteilung Strukturelle Biologie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RANA, C204Homo sapiensMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP358B, D134Homo sapiensMutation(s): 0 
Gene Names: RANBP2, NUP358
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P49792 (Homo sapiens)
Explore P49792 
Go to UniProtKB:  P49792
PHAROS:  P49792
GTEx:  ENSG00000153201 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49792
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
F [auth A],
H [auth C]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.339α = 90
b = 139.463β = 135.78
c = 91.654γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance