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PDBsum Gallery
A random selection of article figures used in PDBsum
The 4 randomly selected references below show some
of the article figures used in PDBsum. Each reference may relate to one or
more PDBsum entries and may be one of the following types:
- key reference - cited in the
JRNL records in the corresponding PDB file,
- secondary reference - listed
in the REMARK records of the corresponding PDB file, or
- added reference - either suggested
by the author(s) or obtained from the journal in question (eg Acta
Cryst D lists related PDB codes on its contents pages).
Note that only figures from the key
and added references are displayed on
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entry's references page, which is reached via the "References" link on
the left.
The figures used are either from Open Access publications or from journals
for which we have obtained permission from the publishers to use their
copyright material.
A maximum of 2 figures are selected from
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J.N.Listgarten,
D.Maes,
L.Wyns,
C.F.Aguilar,
R.A.Palmer.
(1995).
Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 A resolution.
Acta Crystallogr D Biol Crystallogr,
51,
767-771.
[PubMed id: ]
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Figure 2.
Fig. 2. Stereoview of th elecron density
(21/7ol
[Fc[
map contoured at 3)
at the actiesite region in the RNaseA
3',5'dCpdG cocrystallized complex.
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Figure
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1995,
51,
767-771)
copyright 1995.
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PDB entries for which this is a key
reference:
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M.G.Madej,
H.R.Nasiri,
N.S.Hilgendorff,
H.Schwalbe,
C.R.Lancaster.
(2006).
Evidence for transmembrane proton transfer in a dihaem-containing membrane protein complex.
EMBO J,
25,
4963-4970.
[PubMed id: ]
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Figure 1.
Figure 1 Addition of the uncoupler CCCP stimulates the oxidation
of DMNH[2] by fumarate as catalysed by proteoliposomal
E180Q-QFR. (A) Non-functionality of the 'E-pathway' gives rise
to electrogenicity of E180Q-QFR. Subunit A is shown in blue,
subunit B in orange, and subunit C in green. The haem groups are
shown as yellow diamonds, with the upper haem corresponding to
b[P] and the lower one to b[D]. Protons bound are shown in red,
protons released in green. (B) Overall electroneutrality in
wild-type QFR as explained by the 'E-pathway'. For clarity,
protons are indicated to be released to and taken up from the
bulk solvent phase on both sides of the membrane. However, it
can presently not be ruled out that, on either side of the
membrane, the protons are transported along the protein surface
from the respective proton exit sites to those of proton entry,
without being released to the bulk, as argued elsewhere
(Mulkidjanian et al, 2006). (C) DMNH[2] oxidation as (not)
catalysed by E180Q-QFR reconstituted in proteoliposomes (500
 g).
The traces were recorded under the same conditions as for Figure
2A, except that DMNH[2] (20 M)
was used as the electron donor and the fumarate concentration
was 40 M.
Catalytic activity was significantly detectable only after the
addition of 25 M
of the protonophore CCCP. (D) Enlarged section of the left half
of (C). Linear fit of the data points of  A
at t<16 s (grey) and t>16 s (red).
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Figure 3.
Figure 3 The 'E-pathway' in dihaem-containing QFR. Possible
elements of the 'E-pathway' as observed in the crystal structure
of wild-type QFR refined at 1.78 Å resolution (PDB entry
2BS2). To facilitate orientation between various panels, dashed
light blue lines connect the hydroxyl group of residue Tyr C245
to the N  epsilon
atom of His-B215 and the hydroxyl group of Tyr C231 to the C
 atom
of the b[D] ring C propionate. Along these dashed lines, a large
number of polar and protonatable residues can be found. (A, B
(stereo)) Perpendicular views with the periplasm at the bottom,
the cytoplasm at the top and the membrane spanning region
indicated by the two haem groups. In general, carbon, nitrogen
and oxygen atoms are shown in yellow, blue and red,
respectively. In the case of Glu C180, the 'distal' conformer
contains light blue carbon atoms. The groups whose role in such
an 'E-pathway' has received experimental support, Glu C180
(Lancaster et al, 2005; Haas et al, 2005) and the b[D] ring C
propionate (Mileni et al, 2005) are highlighted by purple
ellipsoids. The 2|F[o]|-|F[c]| electron density map, contoured
at 1.0 standard deviations (  )
above the mean density of the map, is shown in blue for the
protein and in green for non-protein groups such as haem groups
and water molecules. (C, D) The transmembrane region as viewed
from the cytoplasmic side. (C) A schematic representation of the
packing of transmembrane helices V and VI, whereas (D) (stereo)
depicts the corresponding view in the structure. The residues
shown on transmembrane helix V are Glu C180 (alternate
conformers), Ser C184 and Tyr C188. Residues shown on
transmembrane helix VI are Tyr C231, Ser C217, Thr C214, Lys
C213, Lys C210, Arg C206 and Asp C203. The residue shown on
transmembrane helix IV is Asp C122.
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Figures
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2006,
25,
4963-4970)
copyright 2006.
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PDB entries for which this is a key
reference:
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U.Okada,
K.Kondo,
T.Hayashi,
N.Watanabe,
M.Yao,
T.Tamura,
I.Tanaka.
(2008).
Structural and functional analysis of the TetR-family transcriptional regulator SCO0332 from Streptomyces coelicolor.
Acta Crystallogr D Biol Crystallogr,
64,
198-205.
[PubMed id: ]
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Figure 1.
Figure 1 Ribbon representation of the SCO0332 dimer. Colour
coding in chain A is from blue (N-terminus) to red (C-terminus).
Chain B is shown in grey. The putative ligand-binding cavities
are shown in marine blue and the loop (Val79'-Ala84') covering
the putative ligand-binding cavity of chain B is coloured
magenta. This figure and the following structural figures were
generated using PyMOL (DeLano Scientific LLC).
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Figure 4.
Figure 4 Putative ligand-binding cavity of SCO0332. (a)
Close-up view of the cavity in chain A. The F[o] - F[c]
difference electron-density map of the uncharacterized ligand
contoured at 2.5  is
shown as a red mesh. A similar density map was also observed in
chain B at the corresponding position. The distances between the
centre points of the electron-density spheres and the N atom of
Gln98 and the O atoms of Tyr136 and Tyr175 are indicated. (b)
Side view of the cavity. The helices are coloured in the same
way as in Fig. 1-. The main chain of the loop (Val79-Ala84) is
coloured magenta and the side chains are shown as stick models
coloured as follows: carbon, magenta; oxygen, red.
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Figures
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2008,
64,
198-205)
copyright 2008.
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PDB entries for which this is a key
reference:
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J.Y.Kim,
M.K.Kim,
G.B.Kang,
C.S.Park,
S.H.Eom.
(2008).
Crystal structure of the leucine zipper domain of small-conductance Ca2+-activated K+ (SK(Ca)) channel from Rattus norvegicus.
Proteins,
70,
568-571.
[PubMed id: ]
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Figure 1.
Figure 1. (A) Stereo view of the SK[Ca] channel LZ trimer
showing heptad residues at a (red) and d (deep blue). (B)
Conserved LZ motifs of various channels in vertebrates and a
typical LZ motif of a transcriptional factor (SK2, SK[Ca]channel
isoform 2; BK, big conductance Ca^2+- and voltage-activated K^+
channels; Ca[V]1.1, voltage-dependent L-type Ca^2+ channel  1S
subunit; RyR2, Ryanodine receptor 2; GCN4, yeast transcriptional
activator). Residues at position d of the heptad repeats are
colored deep blue and residues at position a are colored red.
(C) Helical wheel representation of the LZ trimer. Shown are
residues 488-526 of SK[Ca] channel isoform 2
(NIMYDMISDLNERSEDFEKRIVTLETKLETLIGSIHALP); the view is from the
N-terminus, and residues in the first helical turns are boxed
(Ile489) or circled. Heptad positions are labeled a through g.
Hydrophobic interactions in the core of the helix bundle at
position a and d are connected with blue dashed lines. Hydrogen
pairs between Asn498 at position e and Arg500 at position g are
indicated by red dashed lines across the interhelical interface.
(D) Glutaraldehyde cross-linking assay of LZ domain of the
SK[Ca] channel. The purified LZ domain of rat SK2 channel (lane
1: before cross-linking assay) was incubated with 0.1%
glutaraldehyde for 30 s (lane 2, 4) or 60 s (lane 3, 5). The
concentration of assayed protein was 0.2 mM (lane 2, 3) or 0.6
mM (lane 4, 5). The cross-linking reaction was quenched by
adding sodium dodecyl sulfate (SDS) sample buffer (60 mM
Tris-HCl pH6.8, 25% glycerol, 2% SDS, 14.4 mM  -mercaptoethanol,
0.1% bromophenol) to the final 1×-working concentration.
The cross-linked samples were analyzed by 15% SDS-polyacrylamide
gel electrophoresis.
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Figure
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2008,
70,
568-571)
copyright 2008.
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PDB entries for which this is a key
reference:
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