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 

wwPDB Validation 3D Report Full Report


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

  • 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 ...

    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: 
    • 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
    • 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
    • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAN
A, C
204Homo sapiensMutation(s): 0 
Gene Names: RAN (ARA24)
Find proteins for P62826 (Homo sapiens)
Go to Gene View: RAN
Go to UniProtKB:  P62826
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP358
B, D
134Homo sapiensMutation(s): 0 
Gene Names: RANBP2 (NUP358)
EC: 2.3.2.-
Find proteins for P49792 (Homo sapiens)
Go to Gene View: RANBP2
Go to UniProtKB:  P49792
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A, C
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.339α = 90.00
b = 139.463β = 135.78
c = 91.654γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
XSCALEdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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