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Contents |
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204 a.a.
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134 a.a.
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180 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Complex (small gtpase/nuclear protein)
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Title:
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Structure of the ran-gppnhp-ranbd1 complex
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Structure:
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Ran. Chain: a, c. Engineered: yes. Nuclear pore complex protein nup358. Chain: b, d. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
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Biol. unit:
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Dimer (from
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Resolution:
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2.96Å
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R-factor:
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0.252
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R-free:
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0.304
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Authors:
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I.R.Vetter,C.Nowak,T.Nishimoto,J.Kuhlmann,A.Wittinghofer
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Key ref:
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I.R.Vetter
et al.
(1999).
Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport.
Nature,
398,
39-46.
PubMed id:
DOI:
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Date:
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15-Jan-99
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Release date:
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18-May-99
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PROCHECK
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Headers
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References
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P62826
(RAN_HUMAN) -
GTP-binding nuclear protein Ran
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Seq: Struc:
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216 a.a.
204 a.a.
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Enzyme class:
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Chains B, D:
E.C.5.2.1.8
- Peptidylprolyl isomerase.
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Reaction:
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Peptidylproline (omega=180) = peptidylproline (omega=0)
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Peptidylproline (omega=180)
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=
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peptidylproline (omega=0)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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7 terms
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Biological process
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viral reproduction
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21 terms
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Biochemical function
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nucleotide binding
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7 terms
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DOI no:
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Nature
398:39-46
(1999)
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PubMed id:
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Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport.
|
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I.R.Vetter,
C.Nowak,
T.Nishimoto,
J.Kuhlmann,
A.Wittinghofer.
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ABSTRACT
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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.
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Selected figure(s)
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Figure 1.
Figure 1: Representative electron density around switch I in Ran
dot- GppNHp
and the conserved WKER motif of RanBD1 (residues 57–60).
Residues from RanBD1 are represented by white carbon traces,
residues from Ran by yellow carbon traces. The omit map is
contoured at 1.1 .
The figure was prepared with BOBSCRIPT^46.
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Figure 5.
Figure 5: Molecular embrace and the DEDDDL motif. Surface
representation of RanBD1, showing the basic region where the
DEDDDL motif of Ran is expected to bind after the C terminus
wraps itself around RanBD1. Ran is shown as a backbone (green),
and GppNHp and the magnesium ion as ball and stick. The figure
was produced using GRASP^50.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(1999,
398,
39-46)
copyright 1999.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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Google scholar
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PubMed id
|
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Reference
|
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K.Langer,
C.Dian,
V.Rybin,
C.W.Müller,
and
C.Petosa
(2011).
Insights into the Function of the CRM1 Cofactor RanBP3 from the Structure of Its Ran-Binding Domain.
|
| |
PLoS One, 6,
e17011.
|
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PDB codes:
|
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|
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S.J.Lee,
C.Jiko,
E.Yamashita,
and
T.Tsukihara
(2011).
Selective nuclear export mechanism of small RNAs.
|
| |
Curr Opin Struct Biol, 21,
101-108.
|
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|
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M.Mossalam,
A.S.Dixon,
and
C.S.Lim
(2010).
Controlling subcellular delivery to optimize therapeutic effect.
|
| |
Ther Deliv, 1,
169-193.
|
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|
|
|
|
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M.Yamashita,
K.Kurokawa,
Y.Sato,
A.Yamagata,
H.Mimura,
A.Yoshikawa,
K.Sato,
A.Nakano,
and
S.Fukai
(2010).
Structural basis for the Rho- and phosphoinositide-dependent localization of the exocyst subunit Sec3.
|
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Nat Struct Mol Biol, 17,
180-186.
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PDB code:
|
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R.D.Makde,
J.R.England,
H.P.Yennawar,
and
S.Tan
(2010).
Structure of RCC1 chromatin factor bound to the nucleosome core particle.
|
| |
Nature, 467,
562-566.
|
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PDB code:
|
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|
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S.Terawaki,
K.Kitano,
T.Mori,
Y.Zhai,
Y.Higuchi,
N.Itoh,
T.Watanabe,
K.Kaibuchi,
and
T.Hakoshima
(2010).
The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module.
|
| |
EMBO J, 29,
236-250.
|
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PDB codes:
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J.R.Partridge,
and
T.U.Schwartz
(2009).
Crystallographic and biochemical analysis of the Ran-binding zinc finger domain.
|
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J Mol Biol, 391,
375-389.
|
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PDB codes:
|
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S.G.Brohawn,
J.R.Partridge,
J.R.Whittle,
and
T.U.Schwartz
(2009).
The nuclear pore complex has entered the atomic age.
|
| |
Structure, 17,
1156-1168.
|
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|
|
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|
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T.D.Bunney,
O.Opaleye,
S.M.Roe,
P.Vatter,
R.W.Baxendale,
C.Walliser,
K.L.Everett,
M.B.Josephs,
C.Christow,
F.Rodrigues-Lima,
P.Gierschik,
L.H.Pearl,
and
M.Katan
(2009).
Structural insights into formation of an active signaling complex between Rac and phospholipase C gamma 2.
|
| |
Mol Cell, 34,
223-233.
|
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PDB codes:
|
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|
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T.Zhang,
S.Li,
Y.Zhang,
C.Zhong,
Z.Lai,
and
J.Ding
(2009).
Crystal structure of the ARL2-GTP-BART complex reveals a novel recognition and binding mode of small GTPase with effector.
|
| |
Structure, 17,
602-610.
|
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PDB codes:
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J.Sudhamsu,
G.I.Lee,
D.F.Klessig,
and
B.R.Crane
(2008).
The Structure of YqeH: AN AtNOS1/AtNOA1 ORTHOLOG THAT COUPLES GTP HYDROLYSIS TO MOLECULAR RECOGNITION.
|
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J Biol Chem, 283,
32968-32976.
|
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PDB code:
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N.Schrader,
C.Koerner,
K.Koessmeier,
J.A.Bangert,
A.Wittinghofer,
R.Stoll,
and
I.R.Vetter
(2008).
The crystal structure of the Ran-Nup153ZnF2 complex: a general Ran docking site at the nuclear pore complex.
|
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Structure, 16,
1116-1125.
|
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PDB codes:
|
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N.Schrader,
P.Stelter,
D.Flemming,
R.Kunze,
E.Hurt,
and
I.R.Vetter
(2008).
Structural basis of the nic96 subcomplex organization in the nuclear pore channel.
|
| |
Mol Cell, 29,
46-55.
|
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PDB code:
|
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|
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P.R.Clarke,
and
C.Zhang
(2008).
Spatial and temporal coordination of mitosis by Ran GTPase.
|
| |
Nat Rev Mol Cell Biol, 9,
464-477.
|
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|
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R.Mosca,
B.Brannetti,
and
T.R.Schneider
(2008).
Alignment of protein structures in the presence of domain motions.
|
| |
BMC Bioinformatics, 9,
352.
|
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|
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|
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A.Cook,
F.Bono,
M.Jinek,
and
E.Conti
(2007).
Structural biology of nucleocytoplasmic transport.
|
| |
Annu Rev Biochem, 76,
647-671.
|
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|
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|
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J.Ménétrey,
M.Perderiset,
J.Cicolari,
T.Dubois,
N.Elkhatib,
F.El Khadali,
M.Franco,
P.Chavrier,
and
A.Houdusse
(2007).
Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes.
|
| |
EMBO J, 26,
1953-1962.
|
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PDB code:
|
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M.M.Higa,
S.L.Alam,
W.I.Sundquist,
and
K.S.Ullman
(2007).
Molecular characterization of the Ran-binding zinc finger domain of Nup153.
|
| |
J Biol Chem, 282,
17090-17100.
|
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PDB code:
|
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|
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M.Stewart
(2007).
Molecular mechanism of the nuclear protein import cycle.
|
| |
Nat Rev Mol Cell Biol, 8,
195-208.
|
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|
|
|
|
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A.S.Madrid,
and
K.Weis
(2006).
Nuclear transport is becoming crystal clear.
|
| |
Chromosoma, 115,
98.
|
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|
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|
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C.Rollenhagen,
and
N.Panté
(2006).
Nuclear import of spliceosomal snRNPs.
|
| |
Can J Physiol Pharmacol, 84,
367-376.
|
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|
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|
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K.L.Damm,
and
H.A.Carlson
(2006).
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures.
|
| |
Biophys J, 90,
4558-4573.
|
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|
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|
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L.Brunsveld,
J.Kuhlmann,
K.Alexandrov,
A.Wittinghofer,
R.S.Goody,
and
H.Waldmann
(2006).
Lipidated ras and rab peptides and proteins--synthesis, structure, and function.
|
| |
Angew Chem Int Ed Engl, 45,
6622-6646.
|
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|
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|
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D.B.van Rossum,
R.L.Patterson,
S.Sharma,
R.K.Barrow,
M.Kornberg,
D.L.Gill,
and
S.H.Snyder
(2005).
Phospholipase Cgamma1 controls surface expression of TRPC3 through an intermolecular PH domain.
|
| |
Nature, 434,
99.
|
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|
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F.D.Ciccarelli,
C.von Mering,
M.Suyama,
E.D.Harrington,
E.Izaurralde,
and
P.Bork
(2005).
Complex genomic rearrangements lead to novel primate gene function.
|
| |
Genome Res, 15,
343-351.
|
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|
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|
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K.M.Wagstaff,
M.M.Dias,
G.Alvisi,
and
D.A.Jans
(2005).
Quantitative analysis of protein-protein interactions by native page/fluorimaging.
|
| |
J Fluoresc, 15,
469-473.
|
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|
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M.Lammers,
R.Rose,
A.Scrima,
and
A.Wittinghofer
(2005).
The regulation of mDia1 by autoinhibition and its release by Rho*GTP.
|
| |
EMBO J, 24,
4176-4187.
|
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PDB code:
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R.Riley,
C.Lee,
C.Sabatti,
and
D.Eisenberg
(2005).
Inferring protein domain interactions from databases of interacting proteins.
|
| |
Genome Biol, 6,
R89.
|
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|
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|
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S.Balaji,
M.M.Babu,
L.M.Iyer,
and
L.Aravind
(2005).
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.
|
| |
Nucleic Acids Res, 33,
3994-4006.
|
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|
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|
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S.J.Lee,
Y.Matsuura,
S.M.Liu,
and
M.Stewart
(2005).
Structural basis for nuclear import complex dissociation by RanGTP.
|
| |
Nature, 435,
693-696.
|
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PDB code:
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W.Cho,
and
R.V.Stahelin
(2005).
Membrane-protein interactions in cell signaling and membrane trafficking.
|
| |
Annu Rev Biophys Biomol Struct, 34,
119-151.
|
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|
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A.B.Jaffe,
P.Aspenström,
and
A.Hall
(2004).
Human CNK1 acts as a scaffold protein, linking Rho and Ras signal transduction pathways.
|
| |
Mol Cell Biol, 24,
1736-1746.
|
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|
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C.Blouin,
D.Butt,
and
A.J.Roger
(2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
|
| |
Protein Sci, 13,
608-616.
|
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|
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C.S.Weirich,
J.P.Erzberger,
J.M.Berger,
and
K.Weis
(2004).
The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore.
|
| |
Mol Cell, 16,
749-760.
|
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PDB code:
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D.Engelsma,
R.Bernad,
J.Calafat,
and
M.Fornerod
(2004).
Supraphysiological nuclear export signals bind CRM1 independently of RanGTP and arrest at Nup358.
|
| |
EMBO J, 23,
3643-3652.
|
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|
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|
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E.J.Helmreich
(2004).
Structural flexibility of small GTPases. Can it explain their functional versatility?
|
| |
Biol Chem, 385,
1121-1136.
|
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|
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|
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M.She,
C.J.Decker,
K.Sundramurthy,
Y.Liu,
N.Chen,
R.Parker,
and
H.Song
(2004).
Crystal structure of Dcp1p and its functional implications in mRNA decapping.
|
| |
Nat Struct Mol Biol, 11,
249-256.
|
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PDB code:
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R.Nevo,
V.Brumfeld,
M.Elbaum,
P.Hinterdorfer,
and
Z.Reich
(2004).
Direct discrimination between models of protein activation by single-molecule force measurements.
|
| |
Biophys J, 87,
2630-2634.
|
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|
|
|
|
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Y.Matsuura,
and
M.Stewart
(2004).
Structural basis for the assembly of a nuclear export complex.
|
| |
Nature, 432,
872-877.
|
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|
PDB code:
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|
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A.F.Neuwald,
N.Kannan,
A.Poleksic,
N.Hata,
and
J.S.Liu
(2003).
Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.
|
| |
Genome Res, 13,
673-692.
|
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|
|
|
|
 |
C.Herrmann
(2003).
Ras-effector interactions: after one decade.
|
| |
Curr Opin Struct Biol, 13,
122-129.
|
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|
|
|
|
 |
J.T.Snyder,
A.U.Singer,
M.R.Wing,
T.K.Harden,
and
J.Sondek
(2003).
The pleckstrin homology domain of phospholipase C-beta2 as an effector site for Rac.
|
| |
J Biol Chem, 278,
21099-21104.
|
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|
|
|
|
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J.W.Yu,
and
M.A.Lemmon
(2003).
Genome-wide analysis of signaling domain function.
|
| |
Curr Opin Chem Biol, 7,
103-109.
|
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|
|
|
|
 |
M.J.Seewald,
A.Kraemer,
M.Farkasovsky,
C.Körner,
A.Wittinghofer,
and
I.R.Vetter
(2003).
Biochemical characterization of the Ran-RanBP1-RanGAP system: are RanBP proteins and the acidic tail of RanGAP required for the Ran-RanGAP GTPase reaction?
|
| |
Mol Cell Biol, 23,
8124-8136.
|
 |
|
|
|
|
 |
R.Nevo,
C.Stroh,
F.Kienberger,
D.Kaftan,
V.Brumfeld,
M.Elbaum,
Z.Reich,
and
P.Hinterdorfer
(2003).
A molecular switch between alternative conformational states in the complex of Ran and importin beta1.
|
| |
Nat Struct Biol, 10,
553-557.
|
 |
|
|
|
|
 |
S.Fukai,
H.T.Matern,
J.R.Jagath,
R.H.Scheller,
and
A.T.Brunger
(2003).
Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex.
|
| |
EMBO J, 22,
3267-3278.
|
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|
PDB code:
|
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|
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|
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Z.Ma,
D.A.Hill,
M.H.Collins,
S.W.Morris,
J.Sumegi,
M.Zhou,
C.Zuppan,
and
J.A.Bridge
(2003).
Fusion of ALK to the Ran-binding protein 2 (RANBP2) gene in inflammatory myofibroblastic tumor.
|
| |
Genes Chromosomes Cancer, 37,
98.
|
 |
|
|
|
|
 |
B.F.Volkman,
K.E.Prehoda,
J.A.Scott,
F.C.Peterson,
and
W.A.Lim
(2002).
Structure of the N-WASP EVH1 domain-WIP complex: insight into the molecular basis of Wiskott-Aldrich Syndrome.
|
| |
Cell, 111,
565-576.
|
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|
PDB code:
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|
 |
C.K.Chan,
and
D.A.Jans
(2002).
Using nuclear targeting signals to enhance non-viral gene transfer.
|
| |
Immunol Cell Biol, 80,
119-130.
|
 |
|
|
|
|
 |
K.Plafker,
and
I.G.Macara
(2002).
Fluorescence resonance energy transfer biosensors that detect Ran conformational changes and a Ran x GDP-importin-beta -RanBP1 complex in vitro and in intact cells.
|
| |
J Biol Chem, 277,
30121-30127.
|
 |
|
|
|
|
 |
P.Kalab,
K.Weis,
and
R.Heald
(2002).
Visualization of a Ran-GTP gradient in interphase and mitotic Xenopus egg extracts.
|
| |
Science, 295,
2452-2456.
|
 |
|
|
|
|
 |
R.Pandey,
A.Müller,
C.A.Napoli,
D.A.Selinger,
C.S.Pikaard,
E.J.Richards,
J.Bender,
D.W.Mount,
and
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(2002).
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PDB code:
|
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
| |