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317 a.a.
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133 a.a.
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38 a.a.
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141 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Signaling protein
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Title:
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Crystal structure of the heterotrimeric complex of the rgs domain of rgs9, the gamma subunit of phosphodiesterase and the gt/i1 chimera alpha subunit [(rgs9)-(pdegamma)-(gt/i1alpha)-(gdp)-(alf4-)-(mg2+)]
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Structure:
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Guanine nucleotide-binding protein g(t) subunit alpha-1, guanine nucleotide-binding protein g(i) subunit alpha-1,guanine nucleotide-binding protein g(t) subunit alpha-1. Chain: a, d. Fragment: unp p04695 residues 26-215 and 295-350 linked via unp p10824 residues 220-298. Synonym: transducin alpha-1 chain,adenylate cyclase-inhibiting g alpha protein,transducin alpha-1 chain. Engineered: yes.
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Source:
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Bos taurus, rattus norvegicus. Bovine, rat. Organism_taxid: 9913, 10116. Gene: gnat1, gnai1, gnai-1. Expressed in: escherichia coli. Expression_system_taxid: 562. Bos taurus. Bovine. Organism_taxid: 9913.
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Biol. unit:
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Pentamer (from
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Resolution:
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2.02Å
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R-factor:
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0.233
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R-free:
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0.265
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Authors:
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K.C.Slep,M.A.Kercher,W.He,C.W.Cowan,T.G.Wensel,P.B.Sigler
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Key ref:
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K.C.Slep
et al.
(2001).
Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 A.
Nature,
409,
1071-1077.
PubMed id:
DOI:
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Date:
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05-Sep-00
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Release date:
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28-Feb-01
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PROCHECK
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Headers
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References
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P04695
(GNAT1_BOVIN) -
Guanine nucleotide-binding protein G(t) subunit alpha-1 from Bos taurus
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Seq: Struc:
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350 a.a.
317 a.a.*
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P10824
(GNAI1_RAT) -
Guanine nucleotide-binding protein G(i) subunit alpha-1 from Rattus norvegicus
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Seq: Struc:
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354 a.a.
317 a.a.*
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O46469
(RGS9_BOVIN) -
Regulator of G-protein signaling 9 from Bos taurus
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Seq: Struc:
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484 a.a.
133 a.a.
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Enzyme class 1:
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Chains A, B, D, E:
E.C.?
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Enzyme class 2:
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Chain C:
E.C.3.1.4.35
- 3',5'-cyclic-GMP phosphodiesterase.
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Reaction:
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3',5'-cyclic GMP + H2O = GMP + H+
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3',5'-cyclic GMP
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+
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H2O
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=
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GMP
Bound ligand (Het Group name = )
matches with 85.71% similarity
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+
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H(+)
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Nature
409:1071-1077
(2001)
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PubMed id:
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Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 A.
|
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K.C.Slep,
M.A.Kercher,
W.He,
C.W.Cowan,
T.G.Wensel,
P.B.Sigler.
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ABSTRACT
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A multitude of heptahelical receptors use heterotrimeric G proteins to transduce
signals to specific effector target molecules. The G protein transducin, Gt,
couples photon-activated rhodopsin with the effector cyclic GMP
phosophodiesterase (PDE) in the vertebrate phototransduction cascade. The
interactions of the Gt alpha-subunit (alpha(t)) with the inhibitory PDE
gamma-subunit (PDEgamma) are central to effector activation, and also enhance
visual recovery in cooperation with the GTPase-activating protein regulator of
G-protein signalling (RGS)-9 (refs 1-3). Here we describe the crystal structure
at 2.0 A of rod transducin alpha x GDP x AlF4- in complex with the effector
molecule PDEgamma and the GTPase-activating protein RGS9. In addition, we
present the independently solved crystal structures of the RGS9 RGS domain both
alone and in complex with alpha(t/i1) x GDP x AlF4-. These structures reveal
insights into effector activation, synergistic GTPase acceleration, RGS9
specificity and RGS activity. Effector binding to a nucleotide-dependent site on
alpha(t) sequesters PDEgamma residues implicated in PDE inhibition, and
potentiates recruitment of RGS9 for hydrolytic transition state stabilization
and concomitant signal termination.
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Selected figure(s)
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Figure 3.
Figure 3: PDE bold gamma- /
alpha- [t/i1]
interactions. a, A-weighted
2F[o] - F[c] electron density map for [t/i1]
GDP
AlF^-[4]
PDE
 RGS9
(1.5 ).
Anomalous difference Fourier density (15 )
in coral. b, Intermolecular contact (sub 4 Å) matrix for PDE
residues
(orange) that contact [t/i1]
non-switch residues (green) or [t/i1]
switch residues (blue). Electrostatic interactions to side
chains are shown in red, to main chain in green. van der Waals
contacts to side chains, to main chain or to both are shown in
black, grey and lavender, respectively. Water-mediated
interactions are indicated by blue circles. The root-mean-square
deviation (rmsd) for [t/i1]
contact residues (C atoms
are in black, overall side-chain deviation in grey) is shown for
[t/i1]
RGS9
versus [t]
GTP
S
(left)6 and [t]
GDP
AlF^-[4]
(right)8. Results of PDE alanine
scanning mutagenesis on GTPase stimulation (light-green bars)
and K[A] (dark-blue bars; ref. 13) are shown above. c, C trace
of PDE [50
-87]. C atoms
of residues contacting [t/i1]
switch II, the 3/
3
- 5
loop region or both are in blue, green and orange, respectively.
d, CPK representation of PDE W70
in the switch II/ 3
groove with residues that contact W70 in orange. e, Diagram of
PDE /switch
II/RGS9 interactions coloured as in a. f, CPK representation of
the heterotrimeric complex with the five C-terminal amino acids
of PDE in
red.
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Figure 5.
Figure 5: Interaction modes of the G alpha- switch
II region with G alpha- effector
molecules and the G beta- bold
gamma- subunit.
a, Interaction of PDE with
[t/i1]
GDP
AlF^-[4].
The colouring scheme is the same as in Fig. 1. b, Interaction of
adenylyl cyclase constructs VC[1] (red) and IIC[2] (yellow) with
[s]
GTP
S19.
The [s]
colouring scheme is homologous to that used for [t/i1]
in a. c, Interaction of [259]beta [t] (grey-green) with
[260]alpha [t/i1] [261][glyph.gif] GDP (coloured as in a)23.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2001,
409,
1071-1077)
copyright 2001.
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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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PubMed id
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Reference
|
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A.M.Lyon,
V.M.Tesmer,
V.D.Dhamsania,
D.M.Thal,
J.Gutierrez,
S.Chowdhury,
K.C.Suddala,
J.K.Northup,
and
J.J.Tesmer
(2011).
An autoinhibitory helix in the C-terminal region of phospholipase C-β mediates Gαq activation.
|
| |
Nat Struct Mol Biol,
18,
999.
|
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|
PDB codes:
|
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M.Kosloff,
A.M.Travis,
D.E.Bosch,
D.P.Siderovski,
and
V.Y.Arshavsky
(2011).
Integrating energy calculations with functional assays to decipher the specificity of G protein-RGS protein interactions.
|
| |
Nat Struct Mol Biol,
18,
846-853.
|
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|
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|
|
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A.Yamazaki,
V.A.Bondarenko,
I.Matsuura,
M.Tatsumi,
S.Kurono,
N.Komori,
H.Matsumoto,
F.Hayashi,
R.K.Yamazaki,
and
J.Usukura
(2010).
Mechanism for the regulation of mammalian cGMP phosphodiesterase6. 1: identification of its inhibitory subunit complexes and their roles.
|
| |
Mol Cell Biochem,
339,
215-233.
|
 |
|
|
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|
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A.Zurita,
Y.Zhang,
L.Pedersen,
T.Darden,
and
L.Birnbaumer
(2010).
Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg(2+)-coordinating Thr of regulatory GTPases.
|
| |
Proc Natl Acad Sci U S A,
107,
9596-9601.
|
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B.R.Temple,
C.D.Jones,
and
A.M.Jones
(2010).
Evolution of a signaling nexus constrained by protein interfaces and conformational States.
|
| |
PLoS Comput Biol,
6,
e1000962.
|
 |
|
|
|
|
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G.L.Waldo,
T.K.Ricks,
S.N.Hicks,
M.L.Cheever,
T.Kawano,
K.Tsuboi,
X.Wang,
C.Montell,
T.Kozasa,
J.Sondek,
and
T.K.Harden
(2010).
Kinetic scaffolding mediated by a phospholipase C-beta and Gq signaling complex.
|
| |
Science,
330,
974-980.
|
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|
PDB code:
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J.N.Talbot,
D.L.Roman,
M.J.Clark,
R.A.Roof,
J.J.Tesmer,
R.R.Neubig,
and
J.R.Traynor
(2010).
Differential modulation of mu-opioid receptor signaling to adenylyl cyclase by regulators of G protein signaling proteins 4 or 8 and 7 in permeabilised C6 cells is Galpha subtype dependent.
|
| |
J Neurochem,
112,
1026-1034.
|
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|
|
|
|
 |
L.Dvir,
G.Srour,
R.Abu-Ras,
B.Miller,
S.A.Shalev,
and
T.Ben-Yosef
(2010).
Autosomal-recessive early-onset retinitis pigmentosa caused by a mutation in PDE6G, the gene encoding the gamma subunit of rod cGMP phosphodiesterase.
|
| |
Am J Hum Genet,
87,
258-264.
|
 |
|
|
|
|
 |
L.Shen,
G.Caruso,
P.Bisegna,
D.Andreucci,
V.V.Gurevich,
H.E.Hamm,
and
E.Dibenedetto
(2010).
Dynamics of mouse rod phototransduction and its sensitivity to variation of key parameters.
|
| |
IET Syst Biol,
4,
12.
|
 |
|
|
|
|
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M.Aittaleb,
C.A.Boguth,
and
J.J.Tesmer
(2010).
Structure and function of heterotrimeric G protein-regulated Rho guanine nucleotide exchange factors.
|
| |
Mol Pharmacol,
77,
111-125.
|
 |
|
|
|
|
 |
B.Barren,
L.Gakhar,
H.Muradov,
K.K.Boyd,
S.Ramaswamy,
and
N.O.Artemyev
(2009).
Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit.
|
| |
EMBO J,
28,
3613-3622.
|
 |
|
PDB codes:
|
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|
 |
B.Jastrzebska,
M.Golczak,
D.Fotiadis,
A.Engel,
and
K.Palczewski
(2009).
Isolation and functional characterization of a stable complex between photoactivated rhodopsin and the G protein, transducin.
|
| |
FASEB J,
23,
371-381.
|
 |
|
|
|
|
 |
H.E.Hamm,
S.M.Meier,
G.Liao,
and
A.M.Preininger
(2009).
Trp fluorescence reveals an activation-dependent cation-pi interaction in the Switch II region of Galphai proteins.
|
| |
Protein Sci,
18,
2326-2335.
|
 |
|
|
|
|
 |
K.Khafizov
(2009).
GoLoco motif proteins binding to Galpha(i1): insights from molecular simulations.
|
| |
J Mol Model,
15,
1491-1499.
|
 |
|
|
|
|
 |
L.L.Blazer,
and
R.R.Neubig
(2009).
Small molecule protein-protein interaction inhibitors as CNS therapeutic agents: current progress and future hurdles.
|
| |
Neuropsychopharmacology,
34,
126-141.
|
 |
|
|
|
|
 |
N.Suzuki,
K.Tsumoto,
N.Hajicek,
K.Daigo,
R.Tokita,
S.Minami,
T.Kodama,
T.Hamakubo,
and
T.Kozasa
(2009).
Activation of Leukemia-associated RhoGEF by G{alpha}13 with Significant Conformational Rearrangements in the Interface.
|
| |
J Biol Chem,
284,
5000-5009.
|
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|
|
|
|
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R.Gasper,
S.Meyer,
K.Gotthardt,
M.Sirajuddin,
and
A.Wittinghofer
(2009).
It takes two to tango: regulation of G proteins by dimerization.
|
| |
Nat Rev Mol Cell Biol,
10,
423-429.
|
 |
|
|
|
|
 |
A.Goc,
T.E.Angel,
B.Jastrzebska,
B.Wang,
P.L.Wintrode,
and
K.Palczewski
(2008).
Different properties of the native and reconstituted heterotrimeric G protein transducin.
|
| |
Biochemistry,
47,
12409-12419.
|
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|
|
|
|
 |
A.Shankaranarayanan,
D.M.Thal,
V.M.Tesmer,
D.L.Roman,
R.R.Neubig,
T.Kozasa,
and
J.J.Tesmer
(2008).
Assembly of High Order G{alpha}q-Effector Complexes with RGS Proteins.
|
| |
J Biol Chem,
283,
34923-34934.
|
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|
|
|
|
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C.A.Johnston,
F.S.Willard,
J.K.Ramer,
R.Blaesius,
C.N.Roques,
and
D.P.Siderovski
(2008).
State-selective binding peptides for heterotrimeric G-protein subunits: novel tools for investigating G-protein signaling dynamics.
|
| |
Comb Chem High Throughput Screen,
11,
370-381.
|
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|
|
|
|
 |
C.A.Johnston,
K.Afshar,
J.T.Snyder,
G.G.Tall,
P.Gönczy,
D.P.Siderovski,
and
F.S.Willard
(2008).
Structural determinants underlying the temperature-sensitive nature of a Galpha mutant in asymmetric cell division of Caenorhabditis elegans.
|
| |
J Biol Chem,
283,
21550-21558.
|
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|
PDB codes:
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|
 |
J.Song,
L.W.Guo,
H.Muradov,
N.O.Artemyev,
A.E.Ruoho,
and
J.L.Markley
(2008).
Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure.
|
| |
Proc Natl Acad Sci U S A,
105,
1505-1510.
|
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|
PDB code:
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K.C.Slep,
M.A.Kercher,
T.Wieland,
C.K.Chen,
M.I.Simon,
and
P.B.Sigler
(2008).
Molecular architecture of Galphao and the structural basis for RGS16-mediated deactivation.
|
| |
Proc Natl Acad Sci U S A,
105,
6243-6248.
|
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|
PDB codes:
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|
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K.Sayar,
O.UÄŸur,
T.Liu,
V.J.Hilser,
and
O.Onaran
(2008).
Exploring allosteric coupling in the alpha-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches.
|
| |
BMC Struct Biol,
8,
23.
|
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|
|
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|
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M.L.Cheever,
J.T.Snyder,
S.Gershburg,
D.P.Siderovski,
T.K.Harden,
and
J.Sondek
(2008).
Crystal structure of the multifunctional Gbeta5-RGS9 complex.
|
| |
Nat Struct Mol Biol,
15,
155-162.
|
 |
|
PDB code:
|
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|
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|
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M.Soundararajan,
F.S.Willard,
A.J.Kimple,
A.P.Turnbull,
L.J.Ball,
G.A.Schoch,
C.Gileadi,
O.Y.Fedorov,
E.F.Dowler,
V.A.Higman,
S.Q.Hutsell,
M.Sundström,
D.A.Doyle,
and
D.P.Siderovski
(2008).
Structural diversity in the RGS domain and its interaction with heterotrimeric G protein alpha-subunits.
|
| |
Proc Natl Acad Sci U S A,
105,
6457-6462.
|
 |
|
PDB codes:
|
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|
|
|
|
|
 |
R.J.Austin,
W.W.Ja,
and
R.W.Roberts
(2008).
Evolution of class-specific peptides targeting a hot spot of the Galphas subunit.
|
| |
J Mol Biol,
377,
1406-1418.
|
 |
|
|
|
|
 |
T.G.Wensel
(2008).
Signal transducing membrane complexes of photoreceptor outer segments.
|
| |
Vision Res,
48,
2052-2061.
|
 |
|
|
|
|
 |
W.M.Oldham,
and
H.E.Hamm
(2008).
Heterotrimeric G protein activation by G-protein-coupled receptors.
|
| |
Nat Rev Mol Cell Biol,
9,
60-71.
|
 |
|
|
|
|
 |
Z.Chen,
W.D.Singer,
S.M.Danesh,
P.C.Sternweis,
and
S.R.Sprang
(2008).
Recognition of the activated states of Galpha13 by the rgRGS domain of PDZRhoGEF.
|
| |
Structure,
16,
1532-1543.
|
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|
PDB codes:
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|
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G.X.Xie,
and
P.P.Palmer
(2007).
How regulators of G protein signaling achieve selective regulation.
|
| |
J Mol Biol,
366,
349-365.
|
 |
|
|
|
|
 |
H.Liu,
A.Suresh,
F.S.Willard,
D.P.Siderovski,
S.Lu,
and
N.I.Naqvi
(2007).
Rgs1 regulates multiple Galpha subunits in Magnaporthe pathogenesis, asexual growth and thigmotropism.
|
| |
EMBO J,
26,
690-700.
|
 |
|
|
|
|
 |
S.H.Tsang,
M.L.Woodruff,
L.Jun,
V.Mahajan,
C.K.Yamashita,
R.Pedersen,
C.S.Lin,
S.P.Goff,
T.Rosenberg,
M.Larsen,
D.B.Farber,
and
S.Nusinowitz
(2007).
Transgenic mice carrying the H258N mutation in the gene encoding the beta-subunit of phosphodiesterase-6 (PDE6B) provide a model for human congenital stationary night blindness.
|
| |
Hum Mutat,
28,
243-254.
|
 |
|
|
|
|
 |
W.M.Oldham,
N.Van Eps,
A.M.Preininger,
W.L.Hubbell,
and
H.E.Hamm
(2007).
Mapping allosteric connections from the receptor to the nucleotide-binding pocket of heterotrimeric G proteins.
|
| |
Proc Natl Acad Sci U S A,
104,
7927-7932.
|
 |
|
|
|
|
 |
B.Kreutz,
D.M.Yau,
M.R.Nance,
S.Tanabe,
J.J.Tesmer,
and
T.Kozasa
(2006).
A new approach to producing functional G alpha subunits yields the activated and deactivated structures of G alpha(12/13) proteins.
|
| |
Biochemistry,
45,
167-174.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
C.A.Johnston,
E.S.Lobanova,
A.S.Shavkunov,
J.Low,
J.K.Ramer,
R.Blaesius,
Z.Fredericks,
F.S.Willard,
B.Kuhlman,
V.Y.Arshavsky,
and
D.P.Siderovski
(2006).
Minimal determinants for binding activated G alpha from the structure of a G alpha(i1)-peptide dimer.
|
| |
Biochemistry,
45,
11390-11400.
|
 |
|
PDB code:
|
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|
|
|
|
|
 |
G.B.Willars
(2006).
Mammalian RGS proteins: multifunctional regulators of cellular signalling.
|
| |
Semin Cell Dev Biol,
17,
363-376.
|
 |
|
|
|
|
 |
J.E.Grant,
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PDB code:
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Where a reference describes a PDB structure, the PDB
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');
}
}
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