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PDBsum entry 3c9l
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Signaling protein
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PDB id
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3c9l
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References listed in PDB file
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Key reference
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Title
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Alternative models for two crystal structures of bovine rhodopsin.
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Author
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R.E.Stenkamp.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2008,
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902-904.
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PubMed id
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Abstract
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The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and
2j4y; space group P3(1)) can be re-interpreted as hexagonal (space group P6(4)).
Two molecules of the G protein-coupled receptor are present in the asymmetric
unit in the trigonal models. However, the noncrystallographic twofold axes
parallel to the c axis can be treated as crystallographic symmetry operations in
the hexagonal space group. This halves the asymmetric unit and makes all of the
protein molecules equivalent in these structures. Corrections for merohedral
twinning were also applied in the refinement in the higher symmetry space group
for one of the structures (2j4y).
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Secondary reference #1
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Title
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Structure of bovine rhodopsin in a trigonal crystal form.
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Authors
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J.Li,
P.C.Edwards,
M.Burghammer,
C.Villa,
G.F.Schertler.
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Ref.
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J Mol Biol, 2004,
343,
1409-1438.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. A transmembrane slice showing H-bonding networks
and hydrophobic contacts between the retinal-binding pocket and
the cytoplasmic surface.
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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.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Crystals of native and modified bovine rhodopsins and their heavy atom derivatives.
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Authors
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P.C.Edwards,
J.Li,
M.Burghammer,
J.H.Mcdowell,
C.Villa,
P.A.Hargrave,
G.F.Schertler.
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Ref.
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J Mol Biol, 2004,
343,
1439-1450.
[DOI no: ]
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PubMed id
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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.
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The above figure is
reproduced from the cited reference
with permission from Elsevier
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