 |
PDBsum entry 1gzm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Signaling protein
|
PDB id
|
|
|
|
1gzm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structure of bovine rhodopsin in a trigonal crystal form.
|
|
|
Authors
|
|
J.Li,
P.C.Edwards,
M.Burghammer,
C.Villa,
G.F.Schertler.
|
|
|
Ref.
|
|
J Mol Biol, 2004,
343,
1409-1438.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
We have determined the structure of bovine rhodopsin at 2.65 A resolution using
untwinned native crystals in the space group P3(1), by molecular replacement
from the 2.8 A model (1F88) solved in space group P4(1). The new structure
reveals mechanistically important details unresolved previously, which are
considered in the membrane context by docking the structure into a cryo-electron
microscopy map of 2D crystals. Kinks in the transmembrane helices facilitate
inter-helical polar interactions. Ordered water molecules extend the hydrogen
bonding networks, linking Trp265 in the retinal binding pocket to the NPxxY
motif near the cytoplasmic boundary, and the Glu113 counterion for the
protonated Schiff base to the extracellular surface. Glu113 forms a complex with
a water molecule hydrogen bonded between its main chain and side-chain oxygen
atoms. This can be expected to stabilise the salt-bridge with the protonated
Schiff base linking the 11-cis-retinal to Lys296. The cytoplasmic ends of
helices H5 and H6 have been extended by one turn. The G-protein interaction
sites mapped to the cytoplasmic ends of H5 and H6 and a spiral extension of H5
are elevated above the bilayer. There is a surface cavity next to the conserved
Glu134-Arg135 ion pair. The cytoplasmic loops have the highest temperature
factors in the structure, indicative of their flexibility when not interacting
with G protein or regulatory proteins. An ordered detergent molecule is seen
wrapped around the kink in H6, stabilising the structure around the potential
hinge in H6. These findings provide further explanation for the stability of the
dark state structure. They support a mechanism for the activation, initiated by
photo-isomerisation of the chromophore to its all-trans form, that involves
pivoting movements of kinked helices, which, while maintaining hydrophobic
contacts in the membrane interior, can be coupled to amplified translation of
the helix ends near the membrane surfaces.
|
|
|
|
|
|
|
|
Figure 5.
Figure 5. A transmembrane slice showing H-bonding networks
and hydrophobic contacts between the retinal-binding pocket and
the cytoplasmic surface.
|
|
Figure 6.
Figure 6. Environment of the 11-cis-retinal. (a)
Environment of the protonated Schiff base and its counterion
Glu113. (b) Environment of the ionone ring and the kinks in H6
and H7 cross-linked by a water molecule.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
343,
1409-1438)
copyright 2004.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystals of native and modified bovine rhodopsins and their heavy atom derivatives.
|
|
|
Authors
|
|
P.C.Edwards,
J.Li,
M.Burghammer,
J.H.Mcdowell,
C.Villa,
P.A.Hargrave,
G.F.Schertler.
|
|
|
Ref.
|
|
J Mol Biol, 2004,
343,
1439-1450.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
Figure 5.
Figure 5. Packing arrangement in the P31 crystal of native rhodopsin. (a) Two molecules in the asymmetric unit viewed
along the non-crystallographic 2-fold axis, which passes between the pair of helices 5, one from each molecule, in an
antiparallel orientation. (b) The same molecules rotated with the top towards the viewer by 908 about a horizontal line.
Note the close approach between helices 5 along their entire length. The non-crystallographic 2-fold parallel with the
c-axis (needle axis) of the crystal is now vertical. The C
a
trace is coloured in the rainbow order: H1, dark blue; H2,
light blue; H3, cyan; H4, green; H5, yellow; H6, orange; H7, red; H8, magenta. (c) Stacking of helix bundles in side
view. Single molecules are shown in different colours. Critical C 8E4 molecules are visible wedged between helices of
neighbouring molecules. (d) Stacks of helix bundles in top view. Note the prominent hydrophilic water channel. The
cytoplasmic and extracellular loops protrude undisturbed into this channel. The P31 packing retains an amphiphilic
character similar to the environment in a membrane.
|
|
|
|
|
|
The above figure is
reproduced from the cited reference
with permission from Elsevier
|
|
|
|
|
|
|
